I chose those SNPs (from Moreno et al., 2017):
## no marker haplotype RRR RRR.lower RRR.upper
## 1 1 rs29941 a (39.6%), ref: G (60.4%) 0.5661675 0.3958836 0.8166947
## 2 2 rs2235371 t (5.7%), ref: C (94.3%) 2.3882332 1.2754485 4.3470971
## 3 3 rs4752028 c (22.8%), ref: T (77.2%) 0.7062425 0.5235802 0.9566427
## 4 4 rs633265 t (40.8%), ref: G (59.2%) 0.7236589 0.5211402 0.9914430
## 5 5 rs2912760 t (29.4%), ref: G (70.6%) 0.7332222 0.5328104 0.9955550
## 6 6 rs11084753 a (37.7%), ref: G (62.3%) 0.7267612 0.5118811 1.0389096
## 7 7 rs8001641 g (53.2%), ref: A (46.8%) 1.2971752 0.9682742 1.7447377
## 8 8 rs2912771 g (28%), ref: A (72%) 0.7572373 0.5541278 1.0425273
## 9 9 rs1002246 a (32.6%), ref: G (67.4%) 1.2715154 0.9435431 1.7244731
## 10 10 rs6701037 c (44.8%), ref: A (55.2%) 0.7936407 0.5906322 1.0718157
## 11 11 rs7078160 a (20.6%), ref: G (79.4%) 0.8055953 0.6098222 1.0717973
## 12 12 rs766325 g (46.9%), ref: A (53.1%) 1.2512808 0.9250726 1.7142044
## 13 13 rs4621895 t (41.2%), ref: C (58.8%) 1.2311249 0.9074437 1.6950425
## 14 14 rs470563 c (42%), ref: T (58%) 0.8098298 0.5949561 1.1083503
## 15 15 rs7138803 a (33.4%), ref: G (66.6%) 0.8164243 0.5945113 1.1298432
## 16 16 rs987525 a (21.3%), ref: C (78.7%) 0.8441966 0.6472228 1.1093076
## 17 17 rs3752075 c (35.3%), ref: T (64.7%) 1.1956468 0.8946358 1.6094123
## 18 18 rs17782313 c (20.3%), ref: T (79.7%) 0.8437497 0.6427714 1.1211154
## 19 19 rs7864322 c (32.4%), ref: T (67.6%) 0.8237531 0.5945260 1.1518043
## 20 20 rs571312 a (20.4%), ref: C (79.6%) 0.8503870 0.6463622 1.1336630
## RRR.p.val
## 1 0.002112428
## 2 0.006246328
## 3 0.024213284
## 4 0.046674411
## 5 0.051766208
## 6 0.080862681
## 7 0.081443505
## 8 0.085619288
## 9 0.118744894
## 10 0.126714727
## 11 0.136992528
## 12 0.146070597
## 13 0.182130389
## 14 0.188787688
## 15 0.223087036
## 16 0.225559611
## 17 0.231623488
## 18 0.239445188
## 19 0.254277970
## 20 0.266668447
NOTE: all the genome positions here are from build hg19!
These analyses are for cleft type cntrl!
The data was prepared as in the file: preparing_new_betas_POO_ensembl-db.R, in short:
This gives the following data dimensions:
## rs29941 rs2235371 rs2912760 rs11084753 rs8001641 rs2912771 rs1002246
## [1,] 456 456 456 456 456 456 456
## [2,] 11 14 3 11 1 1 2
## rs6701037 rs766325 rs4621895 rs470563 rs7138803 rs987525
## [1,] 456 456 456 456 456 456
## [2,] 20 19 7 8 11 1
## rs4752028 rs8001641 rs2912771 rs7078160 rs766325 rs470563 rs7138803
## [1,] 456 456 456 456 456 456 456
## [2,] 1 1 1 1 1 1 1
## rs987525 rs3752075 rs7864322
## [1,] 456 456 456
## [2,] 1 1 1
## rs2235371 rs4752028 rs2912760 rs2912771 rs1002246 rs7078160 rs4621895
## [1,] 456 456 456 456 456 456 456
## [2,] 8 3 21 20 28 1 6
## rs470563 rs3752075
## [1,] 456 456
## [2,] 10 16
## Grouping limits, promoter regions:
## rs29941 rs2235371 rs2912760 rs11084753 rs8001641
## 0% -0.8292981 -0.92319540 -0.09432201 -0.8292981 -0.04921919
## 33.33333% 0.1851392 0.07995709 0.93811558 0.1851392 0.97252389
## 66.66667% 0.1888426 0.08121223 0.94738437 0.1888426 0.97689237
## 100% 1.2079032 1.08472736 1.96578368 1.2079032 1.98681766
## rs2912771 rs1002246 rs6701037 rs766325 rs4621895
## 0% -0.06395596 -0.994968313 -0.8698007 -0.96761470 -0.97791111
## 33.33333% 0.96227582 0.008675457 0.1520986 0.04107762 0.04751804
## 66.66667% 0.96900564 0.010691215 0.1656524 0.04505021 0.06177037
## 100% 1.98382246 1.017719637 1.2079442 1.05945242 1.10564412
## rs470563 rs7138803 rs987525
## 0% -0.1947264 -0.8179770 -0.6064441
## 33.33333% 0.8300076 0.1874735 0.7649811
## 66.66667% 0.8377742 0.1891858 0.8186856
## 100% 1.8520632 1.1971780 1.9279907
## Grouping limits, enhancer regions:
## rs4752028 rs8001641 rs2912771 rs7078160 rs766325
## 0% -0.05331135 -0.2760715 -0.2689897 -0.05331135 -0.97800966
## 33.33333% 0.96960934 0.8637778 0.8391328 0.96960934 0.05031837
## 66.66667% 0.97427821 0.8988084 0.8800132 0.97427821 0.06322431
## 100% 1.98548174 1.9626595 1.9533869 1.98548174 1.10677580
## rs470563 rs7138803 rs987525 rs3752075 rs7864322
## 0% -0.97728521 -0.2709916 -0.05647725 -0.97728521 -0.1648839
## 33.33333% 0.04971435 0.8323068 0.96794589 0.04971435 0.9191780
## 66.66667% 0.06542580 0.8566212 0.97227496 0.06542580 0.9378857
## 100% 1.13995296 1.9187266 1.98483253 1.13995296 1.9716043
## Grouping limits, gene regions:
## rs2235371 rs4752028 rs2912760 rs2912771 rs1002246
## 0% -0.4951531 -0.1937871 -0.2520810 -0.2239480 -0.1449001
## 33.33333% 0.5256034 0.8882802 0.7783994 0.7962287 0.8700875
## 66.66667% 0.5334902 0.9109784 0.7852957 0.8033506 0.8737116
## 100% 1.5570875 1.9465224 1.7994528 1.8183151 1.8848442
## rs7078160 rs4621895 rs470563 rs3752075
## 0% -0.05331135 -0.8150516 -0.1737344 -0.1504568
## 33.33333% 0.96960934 0.2137198 0.8601126 0.8771350
## 66.66667% 0.97427821 0.2305664 0.8685060 0.8902507
## 100% 1.98548174 1.2807545 1.8779664 1.9006369
## Choosing the subset of data with only those individuals that we have methylation data for:
## The output file(s) exist!
## Provided arguments:
## --- argument: id, chosen values: 50002, 50004, 50005, 50006, 50008, 50010 ... 51022, 51023, 51026, 51029, 51030, 51031
## INFO: Will select 456 rows and 438 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpWUIZMb/ff5444a437b16.ff
## Saving data...
## ... saved to files: ./data_subset_promoter_GxM_gen.ffData, ./data_subset_promoter_GxM_gen.RData
## Check which SNPs are in the current dataset:
## SNP for gene: rs29941 is in position: 1
## SNP for gene: rs2235371 is in position: 2
## SNP for gene: rs2912760 is in position: 5
## SNP for gene: rs11084753 is in position: 6
## SNP for gene: rs8001641 is in position: 7
## SNP for gene: rs2912771 is in position: 8
## SNP for gene: rs1002246 is in position: 9
## SNP for gene: rs6701037 is in position: 10
## SNP for gene: rs766325 is in position: 12
## SNP for gene: rs4621895 is in position: 13
## SNP for gene: rs470563 is in position: 14
## SNP for gene: rs7138803 is in position: 15
## SNP for gene: rs987525 is in position: 16
##
## HaplinStrat:
## === GENE: rs29941 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 1
## INFO: Will select 456 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac843a25aca.ff
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac86a85209f.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac874fc568b.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
## === GENE: rs2235371 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac852c0428e.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8728178d6.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs2912760 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 5
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8a3f37fe.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac816ae334c.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs11084753 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 6
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac85e343807.ff
## ...done, all alleles: A C
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac868e53bc.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs8001641 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 7
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac86ca2642a.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac872df7ebd.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs2912771 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 8
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac860e25ec8.ff
## ...done, all alleles: C T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac860954228.ff
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "1"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs1002246 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 9
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac81f71a8.ff
## ...done, all alleles: A C
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac84158379c.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs6701037 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 10
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac85da4475.ff
## ...done, all alleles: C T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac85c0236f9.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs766325 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 12
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac85067233d.ff
## ...done, all alleles: C T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac852218e5.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs4621895 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 13
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac85d6e54f3.ff
## ...done, all alleles: A C
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8277b94a.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs470563 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 14
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8166b1ee.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac81c8569d5.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs7138803 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 15
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac86d2e2a68.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac854eb4479.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs987525 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 16
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8485c2d00.ff
## ...done, all alleles: C G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8510c4dea.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: Removed 2 rows containing missing values (geom_errorbar).
## Warning: Removed 2 rows containing missing values (geom_label).
## Warning: Removed 2 rows containing missing values (geom_text).
gxe
test:## --- GENE: rs29941 ---
## ------- GxM: rs29941
## gxe.test chisq df pval
## 1 haplo.freq 3.7636830 2 0.1523094
## 2 child 3.9715995 2 0.1372708
## 3 haplo.freq.trend 0.1881092 1 0.6644950
## 4 child.trend 0.9185717 1 0.3378503
## ------- PoOxM: rs29941
## gxe.test chisq df pval
## 1 haplo.freq 2.317643 2 0.3138558
## 2 poo 2.844592 2 0.2411597
## 3 haplo.freq.trend 1.470274 1 0.2253025
## 4 poo.trend 1.584510 1 0.2081123
## ------
## --- GENE: rs2235371 ---
## ------- GxM: rs2235371
## gxe.test chisq df pval
## 1 haplo.freq 0.3354773 2 0.8455748
## 2 child 0.8012450 2 0.6699029
## 3 haplo.freq.trend 0.3283413 1 0.5666374
## 4 child.trend 0.3641397 1 0.5462161
## ------- PoOxM: rs2235371
## gxe.test chisq df pval
## 1 haplo.freq 3.9654096 2 0.13769629
## 2 poo 4.8607500 2 0.08800383
## 3 haplo.freq.trend 0.0721864 1 0.78817958
## 4 poo.trend 0.1542845 1 0.69447414
## ------
## --- GENE: rs2912760 ---
## ------- GxM: rs2912760
## gxe.test chisq df pval
## 1 haplo.freq 1.34500785 2 0.5104289
## 2 child 2.31601879 2 0.3141108
## 3 haplo.freq.trend 0.01184255 1 0.9133425
## 4 child.trend 0.18062624 1 0.6708356
## ------- PoOxM: rs2912760
## gxe.test chisq df pval
## 1 haplo.freq 0.4840993 2 0.7850172
## 2 poo 1.7654295 2 0.4136584
## 3 haplo.freq.trend 0.4627509 1 0.4963411
## 4 poo.trend 1.1992144 1 0.2734787
## ------
## --- GENE: rs11084753 ---
## ------- GxM: rs11084753
## gxe.test chisq df pval
## 1 haplo.freq 1.822760 2 0.4019690
## 2 child 2.225578 2 0.3286412
## 3 haplo.freq.trend 1.636073 1 0.2008651
## 4 child.trend 1.122299 1 0.2894240
## ------- PoOxM: rs11084753
## gxe.test chisq df pval
## 1 haplo.freq 1.1501148441 2 0.5626726
## 2 poo 0.0004784662 2 0.9997608
## 3 haplo.freq.trend 1.0472957395 1 0.3061307
## 4 poo.trend 0.0004028470 1 0.9839867
## ------
## --- GENE: rs8001641 ---
## ------- GxM: rs8001641
## gxe.test chisq df pval
## 1 haplo.freq 0.5577302 2 0.7566420
## 2 child 3.0856225 2 0.2137793
## 3 haplo.freq.trend 0.3124177 1 0.5762004
## 4 child.trend 0.0022901 1 0.9618318
## ------- PoOxM: rs8001641
## gxe.test chisq df pval
## 1 haplo.freq 0.5115169 2 0.7743290
## 2 poo 0.4540648 2 0.7968950
## 3 haplo.freq.trend 0.1247467 1 0.7239422
## 4 poo.trend 0.1530714 1 0.6956173
## ------
## --- GENE: rs2912771 ---
## ------- GxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 1.535075e-01 2 0.9261179
## 2 child 2.560527e-01 2 0.8798302
## 3 haplo.freq.trend 8.569528e-06 1 0.9976643
## 4 child.trend 7.712945e-06 1 0.9977841
## ------- PoOxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 2.962786e-04 2 0.9998519
## 2 poo 9.475940e-01 2 0.6226336
## 3 haplo.freq.trend 9.365875e-07 1 0.9992278
## 4 poo.trend 9.114716e-01 1 0.3397243
## ------
## --- GENE: rs1002246 ---
## ------- GxM: rs1002246
## gxe.test chisq df pval
## 1 haplo.freq 0.083352933 2 0.9591801
## 2 child 0.334912944 2 0.8458134
## 3 haplo.freq.trend 0.003470487 1 0.9530231
## 4 child.trend 0.002009812 1 0.9642421
## ------- PoOxM: rs1002246
## gxe.test chisq df pval
## 1 haplo.freq 0.4003760 2 0.8185769
## 2 poo 1.9682254 2 0.3737707
## 3 haplo.freq.trend 0.2679789 1 0.6046908
## 4 poo.trend 0.3467907 1 0.5559355
## ------
## --- GENE: rs6701037 ---
## ------- GxM: rs6701037
## gxe.test chisq df pval
## 1 haplo.freq 0.6509612 2 0.7221802
## 2 child 0.5331027 2 0.7660167
## 3 haplo.freq.trend 0.1608618 1 0.6883644
## 4 child.trend 0.2494974 1 0.6174292
## ------- PoOxM: rs6701037
## gxe.test chisq df pval
## 1 haplo.freq 0.38744586 2 0.8238861
## 2 poo 0.91878106 2 0.6316685
## 3 haplo.freq.trend 0.18389256 1 0.6680492
## 4 poo.trend 0.05123373 1 0.8209302
## ------
## --- GENE: rs766325 ---
## ------- GxM: rs766325
## gxe.test chisq df pval
## 1 haplo.freq 0.6184556 2 0.7340136
## 2 child 1.0150473 2 0.6019845
## 3 haplo.freq.trend 0.5357504 1 0.4641993
## 4 child.trend 0.1493877 1 0.6991212
## ------- PoOxM: rs766325
## gxe.test chisq df pval
## 1 haplo.freq 1.214312 2 0.5448983
## 2 poo 1.632597 2 0.4420648
## 3 haplo.freq.trend 1.201938 1 0.2729347
## 4 poo.trend 0.843131 1 0.3585028
## ------
## --- GENE: rs4621895 ---
## ------- GxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 4.128241 2 0.12692989
## 2 child 2.970053 2 0.22649639
## 3 haplo.freq.trend 4.092291 1 0.04307922
## 4 child.trend 2.246711 1 0.13389873
## ------- PoOxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 4.20536723 2 0.12212824
## 2 poo 0.33042918 2 0.84771177
## 3 haplo.freq.trend 3.96824453 1 0.04636609
## 4 poo.trend 0.06403746 1 0.80022475
## ------
## --- GENE: rs470563 ---
## ------- GxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 0.69991581 2 0.7047178
## 2 child 0.29677474 2 0.8620971
## 3 haplo.freq.trend 0.10306982 1 0.7481764
## 4 child.trend 0.01126579 1 0.9154709
## ------- PoOxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 1.3694289627 2 0.5042342
## 2 poo 2.6739888536 2 0.2626338
## 3 haplo.freq.trend 0.0001379167 1 0.9906300
## 4 poo.trend 1.1221859550 1 0.2894482
## ------
## --- GENE: rs7138803 ---
## ------- GxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 0.6979959 2 0.7053946
## 2 child 1.1873637 2 0.5522901
## 3 haplo.freq.trend 0.3300388 1 0.5656362
## 4 child.trend 0.6835803 1 0.4083566
## ------- PoOxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 0.508699574 2 0.7754205
## 2 poo 0.243956037 2 0.8851678
## 3 haplo.freq.trend 0.273801974 1 0.6007927
## 4 poo.trend 0.005188294 1 0.9425782
## ------
## --- GENE: rs987525 ---
## ------- GxM: rs987525
## gxe.test chisq df pval
## 1 haplo.freq 2.659548 2 0.2645370
## 2 child 1.859095 2 0.3947323
## 3 haplo.freq.trend 1.829408 1 0.1761975
## 4 child.trend 1.281560 1 0.2576092
## ------- PoOxM: rs987525
## gxe.test chisq df pval
## 1 haplo.freq 7.981317 2 0.01848754
## 2 poo 4.601209 2 0.10019827
## 3 haplo.freq.trend 5.746210 1 0.01652427
## 4 poo.trend 4.211419 1 0.04015273
## ------
## Choosing the subset of data with only those individuals that we have methylation data for:
## The output file(s) exist!
## Provided arguments:
## --- argument: id, chosen values: 50002, 50004, 50005, 50006, 50008, 50010 ... 51022, 51023, 51026, 51029, 51030, 51031
## INFO: Will select 456 rows and 438 columns.
## Saving data...
## ... saved to files: ./data_subset_enhancer_GxM_gen.ffData, ./data_subset_enhancer_GxM_gen.RData
## Check which SNPs are in the current dataset:
## SNP for gene: rs4752028 is in position: 3
## SNP for gene: rs8001641 is in position: 7
## SNP for gene: rs2912771 is in position: 8
## SNP for gene: rs7078160 is in position: 11
## SNP for gene: rs766325 is in position: 12
## SNP for gene: rs470563 is in position: 14
## SNP for gene: rs7138803 is in position: 15
## SNP for gene: rs987525 is in position: 16
## SNP for gene: rs3752075 is in position: 17
## SNP for gene: rs7864322 is in position: 19
##
## HaplinStrat:
## === GENE: rs4752028 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 3
## INFO: Will select 456 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8697a7823.ff
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac81a658b0.ff
## ...done, all alleles: A T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8434b1336.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs8001641 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 7
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac84a8a3e1e.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8417f5c11.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs2912771 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 8
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac87c1f7af3.ff
## ...done, all alleles: C T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac81aac6905.ff
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "3"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
## === GENE: rs7078160 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 11
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8334d27b6.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac871ae4f49.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs766325 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 12
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac81773972.ff
## ...done, all alleles: C T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8db547f7.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs470563 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 14
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac85ae13c38.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac846c6368e.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs7138803 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 15
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8b5c6d9a.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac842383f70.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs987525 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 16
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8329d2731.ff
## ...done, all alleles: C G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac87f386e65.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs3752075 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 17
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac846d22919.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac833456d16.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs7864322 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 19
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac86b1c5470.ff
## ...done, all alleles: G T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac876b54993.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
gxe
test:## --- GENE: rs4752028 ---
## ------- GxM: rs4752028
## gxe.test chisq df pval
## 1 haplo.freq 7.2395499 2 0.026788705
## 2 child 9.4324034 2 0.008949105
## 3 haplo.freq.trend 0.7494061 1 0.386664338
## 4 child.trend 1.3760550 1 0.240774265
## ------- PoOxM: rs4752028
## gxe.test chisq df pval
## 1 haplo.freq 6.7250357 2 0.03464791
## 2 poo 0.8697576 2 0.64734311
## 3 haplo.freq.trend 0.2772564 1 0.59850514
## 4 poo.trend 0.8686531 1 0.35132845
## ------
## --- GENE: rs8001641 ---
## ------- GxM: rs8001641
## gxe.test chisq df pval
## 1 haplo.freq 1.0459569 2 0.5927524
## 2 child 0.5577513 2 0.7566340
## 3 haplo.freq.trend 0.7703717 1 0.3801021
## 4 child.trend 0.4363365 1 0.5088960
## ------- PoOxM: rs8001641
## gxe.test chisq df pval
## 1 haplo.freq 0.71056444 2 0.7009756
## 2 poo 0.01585769 2 0.9921025
## 3 haplo.freq.trend 0.55195020 1 0.4575219
## 4 poo.trend 0.00673172 1 0.9346093
## ------
## --- GENE: rs2912771 ---
## ------- GxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 0.30700474 2 0.8576987
## 2 child 0.43009141 2 0.8065046
## 3 haplo.freq.trend 0.07899675 1 0.7786616
## 4 child.trend 0.02993271 1 0.8626430
## ------- PoOxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 0.438259666 2 0.8032174
## 2 poo 0.335163926 2 0.8457073
## 3 haplo.freq.trend 0.070369762 1 0.7907992
## 4 poo.trend 0.002417605 1 0.9607845
## ------
## --- GENE: rs7078160 ---
## ------- GxM: rs7078160
## gxe.test chisq df pval
## 1 haplo.freq 0.37695200 2 0.8282204
## 2 child 0.13157349 2 0.9363305
## 3 haplo.freq.trend 0.06763495 1 0.7948119
## 4 child.trend 0.13114354 1 0.7172493
## ------- PoOxM: rs7078160
## gxe.test chisq df pval
## 1 haplo.freq 0.09590338 2 0.9531798
## 2 poo 3.17686651 2 0.2042454
## 3 haplo.freq.trend 0.08044833 1 0.7766908
## 4 poo.trend 1.21028412 1 0.2712759
## ------
## --- GENE: rs766325 ---
## ------- GxM: rs766325
## gxe.test chisq df pval
## 1 haplo.freq 1.77092004 2 0.4125244
## 2 child 1.98858483 2 0.3699851
## 3 haplo.freq.trend 0.06847426 1 0.7935713
## 4 child.trend 0.80701205 1 0.3690051
## ------- PoOxM: rs766325
## gxe.test chisq df pval
## 1 haplo.freq 1.4667123 2 0.4802943
## 2 poo 0.5199581 2 0.7710677
## 3 haplo.freq.trend 0.3126912 1 0.5760334
## 4 poo.trend 0.4853359 1 0.4860153
## ------
## --- GENE: rs470563 ---
## ------- GxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 1.9205176 2 0.3827938
## 2 child 1.1103321 2 0.5739769
## 3 haplo.freq.trend 1.7867419 1 0.1813236
## 4 child.trend 0.2036138 1 0.6518196
## ------- PoOxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 1.74759009 2 0.4173646
## 2 poo 0.79498006 2 0.6720046
## 3 haplo.freq.trend 1.39757976 1 0.2371292
## 4 poo.trend 0.04001606 1 0.8414492
## ------
## --- GENE: rs7138803 ---
## ------- GxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 4.1928312 2 0.1228962
## 2 child 2.3700306 2 0.3057415
## 3 haplo.freq.trend 0.7279389 1 0.3935521
## 4 child.trend 1.6883533 1 0.1938182
## ------- PoOxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 4.684318 2 0.09611989
## 2 poo 1.115459 2 0.57250748
## 3 haplo.freq.trend 1.147999 1 0.28396841
## 4 poo.trend 1.113877 1 0.29124083
## ------
## --- GENE: rs987525 ---
## ------- GxM: rs987525
## gxe.test chisq df pval
## 1 haplo.freq 5.574919 2 0.06157746
## 2 child 6.763480 2 0.03398827
## 3 haplo.freq.trend 5.546923 1 0.01851321
## 4 child.trend 6.215069 1 0.01266674
## ------- PoOxM: rs987525
## gxe.test chisq df pval
## 1 haplo.freq 2.6324113 2 0.268150829
## 2 poo 10.6197725 2 0.004942489
## 3 haplo.freq.trend 0.2987333 1 0.584677623
## 4 poo.trend 6.7103701 1 0.009585383
## ------
## --- GENE: rs3752075 ---
## ------- GxM: rs3752075
## gxe.test chisq df pval
## 1 haplo.freq 2.452410 2 0.2934040
## 2 child 1.331287 2 0.5139427
## 3 haplo.freq.trend 1.207633 1 0.2718014
## 4 child.trend 0.741464 1 0.3891923
## ------- PoOxM: rs3752075
## gxe.test chisq df pval
## 1 haplo.freq 0.95406079 2 0.62062367
## 2 poo 5.06603926 2 0.07941884
## 3 haplo.freq.trend 0.01578338 1 0.90002329
## 4 poo.trend 5.01575345 1 0.02511770
## ------
## --- GENE: rs7864322 ---
## ------- GxM: rs7864322
## gxe.test chisq df pval
## 1 haplo.freq 3.2471286 2 0.19719458
## 2 child 7.5188285 2 0.02329738
## 3 haplo.freq.trend 0.3758561 1 0.53982939
## 4 child.trend 1.5895768 1 0.20738660
## ------- PoOxM: rs7864322
## gxe.test chisq df pval
## 1 haplo.freq 4.9888678 2 0.08254317
## 2 poo 2.1520467 2 0.34094867
## 3 haplo.freq.trend 0.7980590 1 0.37167434
## 4 poo.trend 0.5298324 1 0.46667733
## ------
## Choosing the subset of data with only those individuals that we have methylation data for:
## The output file(s) exist!
## Provided arguments:
## --- argument: id, chosen values: 50002, 50004, 50005, 50006, 50008, 50010 ... 51022, 51023, 51026, 51029, 51030, 51031
## INFO: Will select 456 rows and 438 columns.
## Saving data...
## ... saved to files: ./data_subset_gene_GxM_gen.ffData, ./data_subset_gene_GxM_gen.RData
## Check which SNPs are in the current dataset:
## SNP for gene: rs2235371 is in position: 2
## SNP for gene: rs4752028 is in position: 3
## SNP for gene: rs2912760 is in position: 5
## SNP for gene: rs2912771 is in position: 8
## SNP for gene: rs1002246 is in position: 9
## SNP for gene: rs7078160 is in position: 11
## SNP for gene: rs4621895 is in position: 13
## SNP for gene: rs470563 is in position: 14
## SNP for gene: rs3752075 is in position: 17
##
## HaplinStrat:
## === GENE: rs2235371 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 456 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8412e4cce.ff
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac827297e61.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac89c83d4f.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs4752028 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 3
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac871c0a3e.ff
## ...done, all alleles: A T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac821b5568.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs2912760 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 5
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac83b1357f.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac835121641.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs2912771 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 8
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac85ae84455.ff
## ...done, all alleles: C T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac824c66152.ff
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
## === GENE: rs1002246 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 9
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac810ea7713.ff
## ...done, all alleles: A C
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac83bc57a96.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs7078160 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 11
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac84f4b38b2.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8d8f730d.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs4621895 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 13
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac814355d50.ff
## ...done, all alleles: A C
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8671a233a.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs470563 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 14
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac846e870ac.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac82f5035a5.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: rs3752075 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 17
## INFO: Will select 456 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac81c3514ac.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8178c415a.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 152 152 152
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
gxe
test:## --- GENE: rs2235371 ---
## ------- GxM: rs2235371
## gxe.test chisq df pval
## 1 haplo.freq 4.4757389 2 0.1066856
## 2 child 4.0968645 2 0.1289369
## 3 haplo.freq.trend 0.5216403 1 0.4701428
## 4 child.trend 2.6441340 1 0.1039328
## ------- PoOxM: rs2235371
## gxe.test chisq df pval
## 1 haplo.freq 6.138954 2 0.04644544
## 2 poo 2.458628 2 0.29249319
## 3 haplo.freq.trend 2.004313 1 0.15685233
## 4 poo.trend 1.822782 1 0.17698246
## ------
## --- GENE: rs4752028 ---
## ------- GxM: rs4752028
## gxe.test chisq df pval
## 1 haplo.freq 3.87636841 2 0.1439651
## 2 child 3.12969184 2 0.2091202
## 3 haplo.freq.trend 1.06959608 1 0.3010367
## 4 child.trend 0.04441276 1 0.8330875
## ------- PoOxM: rs4752028
## gxe.test chisq df pval
## 1 haplo.freq 3.5622598084 2 0.1684477
## 2 poo 0.0776294101 2 0.9619289
## 3 haplo.freq.trend 1.0439157251 1 0.3069125
## 4 poo.trend 0.0003263759 1 0.9855863
## ------
## --- GENE: rs2912760 ---
## ------- GxM: rs2912760
## gxe.test chisq df pval
## 1 haplo.freq 0.071771788 2 0.9647504
## 2 child 0.105594449 2 0.9485723
## 3 haplo.freq.trend 0.005239172 1 0.9422978
## 4 child.trend 0.069375426 1 0.7922483
## ------- PoOxM: rs2912760
## gxe.test chisq df pval
## 1 haplo.freq 1.0973791 2 0.5777064
## 2 poo 2.7540075 2 0.2523335
## 3 haplo.freq.trend 0.7824078 1 0.3764058
## 4 poo.trend 1.9089545 1 0.1670794
## ------
## --- GENE: rs2912771 ---
## ------- GxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 0.10531362 2 0.9487055
## 2 child 0.50660204 2 0.7762342
## 3 haplo.freq.trend 0.07430487 1 0.7851690
## 4 child.trend 0.05794693 1 0.8097708
## ------- PoOxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 0.15135909 2 0.9271133
## 2 poo 0.45522943 2 0.7964311
## 3 haplo.freq.trend 0.05750293 1 0.8104871
## 4 poo.trend 0.28073884 1 0.5962174
## ------
## --- GENE: rs1002246 ---
## ------- GxM: rs1002246
## gxe.test chisq df pval
## 1 haplo.freq 4.261124 2 0.11877051
## 2 child 3.200098 2 0.20188664
## 3 haplo.freq.trend 3.872006 1 0.04909780
## 4 child.trend 3.200082 1 0.07363457
## ------- PoOxM: rs1002246
## gxe.test chisq df pval
## 1 haplo.freq 2.4680601 2 0.2911170
## 2 poo 0.6593761 2 0.7191480
## 3 haplo.freq.trend 1.6894432 1 0.1936744
## 4 poo.trend 0.4865921 1 0.4854514
## ------
## --- GENE: rs7078160 ---
## ------- GxM: rs7078160
## gxe.test chisq df pval
## 1 haplo.freq 0.37695200 2 0.8282204
## 2 child 0.13157349 2 0.9363305
## 3 haplo.freq.trend 0.06763495 1 0.7948119
## 4 child.trend 0.13114354 1 0.7172493
## ------- PoOxM: rs7078160
## gxe.test chisq df pval
## 1 haplo.freq 0.09590338 2 0.9531798
## 2 poo 3.17686651 2 0.2042454
## 3 haplo.freq.trend 0.08044833 1 0.7766908
## 4 poo.trend 1.21028412 1 0.2712759
## ------
## --- GENE: rs4621895 ---
## ------- GxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 4.409303 2 0.1102889
## 2 child 3.835832 2 0.1469128
## 3 haplo.freq.trend 3.324415 1 0.0682583
## 4 child.trend 1.535187 1 0.2153356
## ------- PoOxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 4.9576362 2 0.08384226
## 2 poo 0.3856359 2 0.82463209
## 3 haplo.freq.trend 3.8153218 1 0.05078585
## 4 poo.trend 0.3856173 1 0.53461216
## ------
## --- GENE: rs470563 ---
## ------- GxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 1.543498 2 0.4622039
## 2 child 1.321025 2 0.5165864
## 3 haplo.freq.trend 1.379238 1 0.2402311
## 4 child.trend 1.286289 1 0.2567330
## ------- PoOxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 1.2962245 2 0.5230322
## 2 poo 1.2291007 2 0.5408840
## 3 haplo.freq.trend 0.8760903 1 0.3492748
## 4 poo.trend 0.2414018 1 0.6231955
## ------
## --- GENE: rs3752075 ---
## ------- GxM: rs3752075
## gxe.test chisq df pval
## 1 haplo.freq 3.364759 2 0.18593101
## 2 child 7.238165 2 0.02680726
## 3 haplo.freq.trend 2.429652 1 0.11905935
## 4 child.trend 5.672619 1 0.01723171
## ------- PoOxM: rs3752075
## gxe.test chisq df pval
## 1 haplo.freq 1.3076783 2 0.5200454
## 2 poo 1.5091820 2 0.4702029
## 3 haplo.freq.trend 0.6044755 1 0.4368755
## 4 poo.trend 1.4256081 1 0.2324825
## ------
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Saved image to file: GxM_PoOxM_new_betas_mult_top-SNPs-PoO-scan_ cntrl .RData