GxM, betas, multiplicative model, using top 20 SNPs from PoO scan
Julia Romanowska
2019-10-17
Introduction
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 0.266668447NOTE: all the genome positions here are from build hg19!
These analyses are for cleft type CLP!
Data preparations
The data was prepared as in the file: preparing_new_betas_POO_ensembl-db.R, in short:
- identification of promoter and enhancer regions around the chosen SNPs, based on the regulatory ensembl database (build 37),
- extracting the matching data from both datasets, genomic and methylation
This gives the following data dimensions:
- for the promoter region:
## rs29941 rs2235371 rs2912760 rs11084753 rs8001641 rs2912771 rs1002246
## [1,] 166 166 166 166 166 166 166
## [2,] 11 14 3 11 1 1 2
## rs6701037 rs766325 rs4621895 rs470563 rs7138803 rs987525
## [1,] 166 166 166 166 166 166
## [2,] 20 19 7 8 11 1- for the enhancer region:
## rs4752028 rs8001641 rs2912771 rs7078160 rs766325 rs470563 rs7138803
## [1,] 166 166 166 166 166 166 166
## [2,] 1 1 1 1 1 1 1
## rs987525 rs3752075 rs7864322
## [1,] 166 166 166
## [2,] 1 1 1- for the gene region:
## rs2235371 rs4752028 rs2912760 rs2912771 rs1002246 rs7078160 rs4621895
## [1,] 166 166 166 166 166 166 166
## [2,] 8 3 21 20 28 1 6
## rs470563 rs3752075
## [1,] 166 166
## [2,] 10 16Categorizing methylation values
- sum up and average the beta values from all CpGs within the region
- divide into three categories: low, medium and high values
Divide the individuals in three groups (created by calculating the 33% and 66% quantiles)
## Grouping limits, promoter regions:## rs29941 rs2235371 rs2912760 rs11084753 rs8001641
## 0% -0.8265624 -0.92332957 -0.09730081 -0.8265624 -0.04859895
## 33.33333% 0.1852513 0.08042859 0.93838143 0.1852513 0.97459638
## 66.66667% 0.1895493 0.08160429 0.94756641 0.1895493 0.97844535
## 100% 1.2007892 1.08475254 1.96376129 1.2007892 1.98594815
## rs2912771 rs1002246 rs6701037 rs766325 rs4621895
## 0% -0.05331546 -0.995090693 -0.8710708 -0.96691483 -0.96989876
## 33.33333% 0.96309501 0.008648142 0.1538774 0.04258831 0.04878925
## 66.66667% 0.96916562 0.010653654 0.1654468 0.04723040 0.06107890
## 100% 1.98039806 1.015095182 1.2022087 1.06086396 1.10573687
## rs470563 rs7138803 rs987525
## 0% -0.1862420 -0.8159564 -0.6060226
## 33.33333% 0.8302055 0.1875254 0.7508203
## 66.66667% 0.8381480 0.1893247 0.8244217
## 100% 1.8499218 1.1943410 1.9248418## Grouping limits, enhancer regions:## rs4752028 rs8001641 rs2912771 rs7078160 rs766325
## 0% -0.05018514 -0.2352023 -0.3189679 -0.05018514 -0.97289033
## 33.33333% 0.97082043 0.8727414 0.8320234 0.97082043 0.05056198
## 66.66667% 0.97487551 0.8990984 0.8747457 0.97487551 0.06311021
## 100% 1.98267764 1.9566071 1.9385253 1.98267764 1.10194979
## rs470563 rs7138803 rs987525 rs3752075 rs7864322
## 0% -0.96840456 -0.2496715 -0.05056983 -0.96840456 -0.1587498
## 33.33333% 0.05339005 0.8224549 0.96851492 0.05339005 0.9212322
## 66.66667% 0.07273451 0.8470730 0.97285628 0.07273451 0.9396470
## 100% 1.12376346 1.9117069 1.98034143 1.12376346 1.9683288## Grouping limits, gene regions:## rs2235371 rs4752028 rs2912760 rs2912771 rs1002246
## 0% -0.4962427 -0.1577492 -0.2435622 -0.2304825 -0.1462102
## 33.33333% 0.5271026 0.8962173 0.7796299 0.7951135 0.8695090
## 66.66667% 0.5329545 0.9126078 0.7872902 0.8033183 0.8730066
## 100% 1.5546907 1.9402612 1.8011469 1.8179549 1.8784302
## rs7078160 rs4621895 rs470563 rs3752075
## 0% -0.05018514 -0.8062911 -0.1784037 -0.1504040
## 33.33333% 0.97082043 0.2160658 0.8616054 0.8799055
## 66.66667% 0.97487551 0.2291484 0.8696969 0.8899844
## 100% 1.98267764 1.2849581 1.8766888 1.8981752Running haplinStrat
Promoter regions
## Choosing the subset of data with only those individuals that we have methylation data for:## Provided arguments:
## --- argument: id, chosen values: 1, 5, 8, 13, 15, 19 ... 671, 672, 675, 682, 683, 684
## INFO: Will select 166 rows and 438 columns.## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpWUIZMb/ff5445c8a4be4.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:
## Provided arguments:
## --- chosen markers: 1
## INFO: Will select 166 rows and 6 columns.## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc4e0a5ef7.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:
## 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/Rtmp6jNl5G/ff26bc48a9769e.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc6e272b4a.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
## 56 55 55
##
## 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: rs2235371 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 166 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/Rtmp6jNl5G/ff26bc41a065fb.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc18375cad.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc38665ef.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bce662ad.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
## 56 55 55
##
## 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: rs11084753 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 6
## INFO: Will select 166 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/Rtmp6jNl5G/ff26bc4342208d.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc1a502cbf.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc265f609c.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc64d86aee.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc1a4b3a17.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc31a42258.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
## 56 55 55
##
## 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: rs1002246 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 9
## INFO: Will select 166 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/Rtmp6jNl5G/ff26bc227a22ae.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc751c11af.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc73c11a43.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc296e65b9.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc6adb36e.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc410d3dd1.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc12e74bf9.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc292e64.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc3be86564.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc5c497f74.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc2143d62.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc49e6d18.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc2045665b.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc2eae1ffa.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
## 56 55 55
##
## 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- plotting results:
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: Removed 3 rows containing missing values (geom_errorbar).## Warning: Removed 3 rows containing missing values (geom_label).## Warning: Removed 3 rows containing missing values (geom_text).
gxetest:
## --- GENE: rs29941 ---
## ------- GxM: rs29941
## gxe.test chisq df pval
## 1 haplo.freq 1.502486373 2 0.4717797
## 2 child 0.380996482 2 0.8265472
## 3 haplo.freq.trend 0.001580504 1 0.9682880
## 4 child.trend 0.028005903 1 0.8670949
## ------- PoOxM: rs29941
## gxe.test chisq df pval
## 1 haplo.freq 2.7834105 2 0.2486509
## 2 poo 1.6455231 2 0.4392171
## 3 haplo.freq.trend 0.3154108 1 0.5743787
## 4 poo.trend 1.1215717 1 0.2895803
## ------
## --- GENE: rs2235371 ---
## ------- GxM: rs2235371
## gxe.test chisq df pval
## 1 haplo.freq 1.3508133 2 0.5089494
## 2 child 0.8024579 2 0.6694968
## 3 haplo.freq.trend 1.3431962 1 0.2464711
## 4 child.trend 0.6094472 1 0.4349960
## ------- PoOxM: rs2235371
## gxe.test chisq df pval
## 1 haplo.freq 0.7860510493 2 0.6750115
## 2 poo 4.5875091487 2 0.1008870
## 3 haplo.freq.trend 0.0009718357 1 0.9751306
## 4 poo.trend 2.6014242205 1 0.1067677
## ------
## --- GENE: rs2912760 ---
## ------- GxM: rs2912760
## gxe.test chisq df pval
## 1 haplo.freq 2.966581 2 0.22688991
## 2 child 2.998177 2 0.22333362
## 3 haplo.freq.trend 2.942351 1 0.08628505
## 4 child.trend 2.875739 1 0.08992367
## ------- PoOxM: rs2912760
## gxe.test chisq df pval
## 1 haplo.freq 1.162866 2 0.5590967
## 2 poo 2.175056 2 0.3370487
## 3 haplo.freq.trend 1.157962 1 0.2818886
## 4 poo.trend 1.173397 1 0.2787044
## ------
## --- GENE: rs11084753 ---
## ------- GxM: rs11084753
## gxe.test chisq df pval
## 1 haplo.freq 2.19608798 2 0.33352282
## 2 child 6.93619118 2 0.03117635
## 3 haplo.freq.trend 0.03239430 1 0.85716501
## 4 child.trend 0.01572096 1 0.90022015
## ------- PoOxM: rs11084753
## gxe.test chisq df pval
## 1 haplo.freq 0.07916692 2 0.9611897
## 2 poo 3.99155046 2 0.1359083
## 3 haplo.freq.trend 0.07753416 1 0.7806673
## 4 poo.trend 0.71104212 1 0.3990981
## ------
## --- GENE: rs8001641 ---
## ------- GxM: rs8001641
## gxe.test chisq df pval
## 1 haplo.freq 6.847776 2 0.03258550
## 2 child 4.893777 2 0.08656249
## 3 haplo.freq.trend 4.060834 1 0.04388882
## 4 child.trend 3.130796 1 0.07682620
## ------- PoOxM: rs8001641
## gxe.test chisq df pval
## 1 haplo.freq 8.021989 2 0.018115369
## 2 poo 7.509129 2 0.023410643
## 3 haplo.freq.trend 7.553240 1 0.005990227
## 4 poo.trend 3.626403 1 0.056869601
## ------
## --- GENE: rs2912771 ---
## ------- GxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 2.100041e-05 2 0.9999895
## 2 child 2.018149e-05 2 0.9999899
## 3 haplo.freq.trend 5.307412e-11 1 0.9999942
## 4 child.trend 7.007132e-09 1 0.9999332
## ------- PoOxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 2.042490e-05 2 0.9999898
## 2 poo 1.018521e-05 2 0.9999949
## 3 haplo.freq.trend 2.469284e-10 1 0.9999875
## 4 poo.trend 6.999300e-06 1 0.9978891
## ------
## --- GENE: rs1002246 ---
## ------- GxM: rs1002246
## gxe.test chisq df pval
## 1 haplo.freq 0.36406026 2 0.8335762
## 2 child 0.40423109 2 0.8170005
## 3 haplo.freq.trend 0.02765315 1 0.8679269
## 4 child.trend 0.31142197 1 0.5768089
## ------- PoOxM: rs1002246
## gxe.test chisq df pval
## 1 haplo.freq 0.2673879 2 0.8748578
## 2 poo 2.2950566 2 0.3174204
## 3 haplo.freq.trend 0.2533673 1 0.6147140
## 4 poo.trend 0.7767824 1 0.3781270
## ------
## --- GENE: rs6701037 ---
## ------- GxM: rs6701037
## gxe.test chisq df pval
## 1 haplo.freq 0.75198168 2 0.6866086
## 2 child 0.17298027 2 0.9171446
## 3 haplo.freq.trend 0.10090259 1 0.7507492
## 4 child.trend 0.07357708 1 0.7861980
## ------- PoOxM: rs6701037
## gxe.test chisq df pval
## 1 haplo.freq 0.80039834 2 0.6701866
## 2 poo 0.12189743 2 0.9408715
## 3 haplo.freq.trend 0.12592067 1 0.7226997
## 4 poo.trend 0.09757977 1 0.7547536
## ------
## --- GENE: rs766325 ---
## ------- GxM: rs766325
## gxe.test chisq df pval
## 1 haplo.freq 0.08707738 2 0.9573955
## 2 child 1.03194827 2 0.5969188
## 3 haplo.freq.trend 0.06639662 1 0.7966574
## 4 child.trend 0.54320795 1 0.4611063
## ------- PoOxM: rs766325
## gxe.test chisq df pval
## 1 haplo.freq 5.302920 2 0.0705481271
## 2 poo 14.688161 2 0.0006464076
## 3 haplo.freq.trend 5.118868 1 0.0236670451
## 4 poo.trend 14.524439 1 0.0001383530
## ------
## --- GENE: rs4621895 ---
## ------- GxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 2.635098028 2 0.2677908
## 2 child 2.250406889 2 0.3245864
## 3 haplo.freq.trend 0.062966467 1 0.8018673
## 4 child.trend 0.002485679 1 0.9602367
## ------- PoOxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 2.4557492 2 0.2929145
## 2 poo 0.1840768 2 0.9120701
## 3 haplo.freq.trend 0.1238991 1 0.7248435
## 4 poo.trend 0.1102742 1 0.7398322
## ------
## --- GENE: rs470563 ---
## ------- GxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 4.031417 2 0.13322597
## 2 child 3.680337 2 0.15879066
## 3 haplo.freq.trend 3.547768 1 0.05962562
## 4 child.trend 2.227265 1 0.13559364
## ------- PoOxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 2.446649 2 0.2942503
## 2 poo 2.335468 2 0.3110711
## 3 haplo.freq.trend 2.349958 1 0.1252864
## 4 poo.trend 1.873521 1 0.1710723
## ------
## --- GENE: rs7138803 ---
## ------- GxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 0.29138931 2 0.8644216
## 2 child 0.04700078 2 0.9767736
## 3 haplo.freq.trend 0.08077199 1 0.7762539
## 4 child.trend 0.04378586 1 0.8342525
## ------- PoOxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 0.3603815 2 0.8351109
## 2 poo 0.5194453 2 0.7712655
## 3 haplo.freq.trend 0.1714687 1 0.6788098
## 4 poo.trend 0.4943508 1 0.4819929
## ------
## --- GENE: rs987525 ---
## ------- GxM: rs987525
## gxe.test chisq df pval
## 1 haplo.freq 1.1246873 2 0.5698719
## 2 child 2.0584513 2 0.3572835
## 3 haplo.freq.trend 0.4866585 1 0.4854217
## 4 child.trend 0.1541149 1 0.6946336
## ------- PoOxM: rs987525
## gxe.test chisq df pval
## 1 haplo.freq 0.58803262 2 0.7452643
## 2 poo 1.00895109 2 0.6038222
## 3 haplo.freq.trend 0.46117395 1 0.4970758
## 4 poo.trend 0.07849031 1 0.7793538
## ------Enhancer regions
## Choosing the subset of data with only those individuals that we have methylation data for:## Provided arguments:
## --- argument: id, chosen values: 1, 5, 8, 13, 15, 19 ... 671, 672, 675, 682, 683, 684
## INFO: Will select 166 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:
## Provided arguments:
## --- chosen markers: 3
## INFO: Will select 166 rows and 6 columns.## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bcbbd27d8.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:
## 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/Rtmp6jNl5G/ff26bc18c05baf.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc1c7a1a8a.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc332a5649.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc2929684e.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
## 56 55 55
##
## 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: rs2912771 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 8
## INFO: Will select 166 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/Rtmp6jNl5G/ff26bc5b907bf5.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc1e9476da.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
## 56 55 55
##
## 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: rs7078160 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 11
## INFO: Will select 166 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/Rtmp6jNl5G/ff26bc5008ad7.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc1d9e720c.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc7aa82268.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc7e8fdf9.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
## 56 55 55
##
## 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: rs470563 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 14
## INFO: Will select 166 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/Rtmp6jNl5G/ff26bc4c0d4ff4.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc7911f66.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc25d56b1a.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc3331450.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc5524424f.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc6e45c65.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc1d23175b.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc79801189.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
## 56 55 55
##
## 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: rs7864322 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 19
## INFO: Will select 166 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/Rtmp6jNl5G/ff26bc517c6bdb.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc69bf3052.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
## 56 55 55
##
## 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- plotting results:
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: Removed 3 rows containing missing values (geom_errorbar).## Warning: Removed 3 rows containing missing values (geom_label).## Warning: Removed 3 rows containing missing values (geom_text).
gxetest:
## --- GENE: rs4752028 ---
## ------- GxM: rs4752028
## gxe.test chisq df pval
## 1 haplo.freq 3.104146e-01 2 0.8562377
## 2 child 1.156040e-01 2 0.9438368
## 3 haplo.freq.trend 1.118667e-13 1 0.9999997
## 4 child.trend 1.296325e-02 1 0.9093517
## ------- PoOxM: rs4752028
## gxe.test chisq df pval
## 1 haplo.freq 0.3191192 2 0.8525191
## 2 poo 1.2858737 2 0.5257461
## 3 haplo.freq.trend 0.1584837 1 0.6905564
## 4 poo.trend 1.2533553 1 0.2629126
## ------
## --- GENE: rs8001641 ---
## ------- GxM: rs8001641
## gxe.test chisq df pval
## 1 haplo.freq 1.73747704 2 0.4194804
## 2 child 1.18484648 2 0.5529856
## 3 haplo.freq.trend 0.53899156 1 0.4628510
## 4 child.trend 0.03954208 1 0.8423786
## ------- PoOxM: rs8001641
## gxe.test chisq df pval
## 1 haplo.freq 1.1856517 2 0.55276306
## 2 poo 5.5457901 2 0.06248086
## 3 haplo.freq.trend 0.8278745 1 0.36288786
## 4 poo.trend 0.2913018 1 0.58938749
## ------
## --- GENE: rs2912771 ---
## ------- GxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 2.069314e-05 2 0.9999897
## 2 child 1.989348e-05 2 0.9999901
## 3 haplo.freq.trend 1.072361e-05 1 0.9973872
## 4 child.trend 1.071198e-05 1 0.9973886
## ------- PoOxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 2.015462e-05 2 0.9999899
## 2 poo 1.004640e-05 2 0.9999950
## 3 haplo.freq.trend 1.071917e-05 1 0.9973877
## 4 poo.trend 3.154870e-06 1 0.9985828
## ------
## --- GENE: rs7078160 ---
## ------- GxM: rs7078160
## gxe.test chisq df pval
## 1 haplo.freq 2.2976761 2 0.3170049
## 2 child 0.9955490 2 0.6078820
## 3 haplo.freq.trend 0.5405068 1 0.4622228
## 4 child.trend 0.5881063 1 0.4431523
## ------- PoOxM: rs7078160
## gxe.test chisq df pval
## 1 haplo.freq 4.50679044 2 0.1050420
## 2 poo 2.78075748 2 0.2489810
## 3 haplo.freq.trend 0.32439948 1 0.5689756
## 4 poo.trend 0.02753357 1 0.8682101
## ------
## --- GENE: rs766325 ---
## ------- GxM: rs766325
## gxe.test chisq df pval
## 1 haplo.freq 0.526788980 2 0.7684387
## 2 child 0.042823332 2 0.9788159
## 3 haplo.freq.trend 0.515230951 1 0.4728831
## 4 child.trend 0.003549476 1 0.9524922
## ------- PoOxM: rs766325
## gxe.test chisq df pval
## 1 haplo.freq 0.41909825 2 0.8109498
## 2 poo 0.39943715 2 0.8189612
## 3 haplo.freq.trend 0.15995401 1 0.6891989
## 4 poo.trend 0.08051657 1 0.7765986
## ------
## --- GENE: rs470563 ---
## ------- GxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 1.8040841 2 0.4057403
## 2 child 1.7515323 2 0.4165428
## 3 haplo.freq.trend 0.7891165 1 0.3743674
## 4 child.trend 1.5774335 1 0.2091308
## ------- PoOxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 1.42132187 2 0.4913194
## 2 poo 2.03069490 2 0.3622765
## 3 haplo.freq.trend 0.08498163 1 0.7706566
## 4 poo.trend 1.95599042 1 0.1619428
## ------
## --- GENE: rs7138803 ---
## ------- GxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 3.776470 2 0.15133866
## 2 child 2.987379 2 0.22454267
## 3 haplo.freq.trend 3.499613 1 0.06138317
## 4 child.trend 2.945326 1 0.08612631
## ------- PoOxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 3.507808687 2 0.17309679
## 2 poo 1.678933771 2 0.43194074
## 3 haplo.freq.trend 3.426435093 1 0.06416046
## 4 poo.trend 0.001730206 1 0.96682096
## ------
## --- GENE: rs987525 ---
## ------- GxM: rs987525
## gxe.test chisq df pval
## 1 haplo.freq 1.1726987 2 0.5563546
## 2 child 0.7635618 2 0.6826446
## 3 haplo.freq.trend 0.1633887 1 0.6860556
## 4 child.trend 0.6687907 1 0.4134735
## ------- PoOxM: rs987525
## gxe.test chisq df pval
## 1 haplo.freq 0.5499656 2 0.7595852
## 2 poo 4.1598762 2 0.1249379
## 3 haplo.freq.trend 0.5146373 1 0.4731383
## 4 poo.trend 0.9647304 1 0.3259979
## ------
## --- GENE: rs3752075 ---
## ------- GxM: rs3752075
## gxe.test chisq df pval
## 1 haplo.freq 1.957710 2 0.37574108
## 2 child 3.969997 2 0.13738084
## 3 haplo.freq.trend 1.957707 1 0.16175876
## 4 child.trend 3.921631 1 0.04766862
## ------- PoOxM: rs3752075
## gxe.test chisq df pval
## 1 haplo.freq 0.3317706 2 0.8471434
## 2 poo 1.0085013 2 0.6039580
## 3 haplo.freq.trend 0.3092368 1 0.5781489
## 4 poo.trend 0.5643093 1 0.4525291
## ------
## --- GENE: rs7864322 ---
## ------- GxM: rs7864322
## gxe.test chisq df pval
## 1 haplo.freq 5.533540 2 0.06286473
## 2 child 3.881713 2 0.14358089
## 3 haplo.freq.trend 5.477272 1 0.01926531
## 4 child.trend 2.585337 1 0.10785748
## ------- PoOxM: rs7864322
## gxe.test chisq df pval
## 1 haplo.freq 5.31725309 2 0.07004436
## 2 poo 1.29676592 2 0.52289063
## 3 haplo.freq.trend 5.26316330 1 0.02178140
## 4 poo.trend 0.03958239 1 0.84229933
## ------Gene regions
## Choosing the subset of data with only those individuals that we have methylation data for:## Provided arguments:
## --- argument: id, chosen values: 1, 5, 8, 13, 15, 19 ... 671, 672, 675, 682, 683, 684
## INFO: Will select 166 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:
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 166 rows and 6 columns.## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc24bf108c.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:
## 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/Rtmp6jNl5G/ff26bc720112e1.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc20407ced.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
## 56 55 55
##
## 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: rs4752028 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 3
## INFO: Will select 166 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/Rtmp6jNl5G/ff26bc6011382b.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc6d6175a.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc6f174c93.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc74a95820.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc77ae16bd.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc5f1b1f15.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
## 56 55 55
##
## 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: rs1002246 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 9
## INFO: Will select 166 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/Rtmp6jNl5G/ff26bc5a194abc.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc77bf1b5f.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
## 56 55 55
##
## 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: rs7078160 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 11
## INFO: Will select 166 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/Rtmp6jNl5G/ff26bc5cba6a9a.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc462167fb.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc1a9c76d4.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc38d1183a.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc1ea6edc.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc5fe1243f.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
## 56 55 55
##
## 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 166 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/Rtmp6jNl5G/ff26bc62762195.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
## 56 55 55
##
## Running Haplin on full data file...## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp6jNl5G/ff26bc37692582.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
## 56 55 55
##
## 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- plotting results:
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: Removed 3 rows containing missing values (geom_errorbar).## Warning: Removed 3 rows containing missing values (geom_label).## Warning: Removed 3 rows containing missing values (geom_text).
gxetest:
## --- GENE: rs2235371 ---
## ------- GxM: rs2235371
## gxe.test chisq df pval
## 1 haplo.freq 1.3748371 2 0.5028725
## 2 child 2.5307102 2 0.2821391
## 3 haplo.freq.trend 1.0058725 1 0.3158937
## 4 child.trend 0.5590205 1 0.4546552
## ------- PoOxM: rs2235371
## gxe.test chisq df pval
## 1 haplo.freq 0.06611478 2 0.9674830
## 2 poo 1.14909536 2 0.5629594
## 3 haplo.freq.trend 0.06490628 1 0.7989030
## 4 poo.trend 0.72512093 1 0.3944693
## ------
## --- GENE: rs4752028 ---
## ------- GxM: rs4752028
## gxe.test chisq df pval
## 1 haplo.freq 0.41227866 2 0.8137197
## 2 child 0.75637455 2 0.6851022
## 3 haplo.freq.trend 0.05794283 1 0.8097774
## 4 child.trend 0.37662301 1 0.5394161
## ------- PoOxM: rs4752028
## gxe.test chisq df pval
## 1 haplo.freq 5.2857997 2 0.07115463
## 2 poo 4.8221700 2 0.08971790
## 3 haplo.freq.trend 0.2097700 1 0.64694772
## 4 poo.trend 0.4774054 1 0.48959991
## ------
## --- GENE: rs2912760 ---
## ------- GxM: rs2912760
## gxe.test chisq df pval
## 1 haplo.freq 0.0304581355 2 0.9848863
## 2 child 0.1909691126 2 0.9089324
## 3 haplo.freq.trend 0.0000114583 1 0.9972992
## 4 child.trend 0.1813521003 1 0.6702138
## ------- PoOxM: rs2912760
## gxe.test chisq df pval
## 1 haplo.freq 0.2373838 2 0.8880814
## 2 poo 1.0056402 2 0.6048226
## 3 haplo.freq.trend 0.2207907 1 0.6384381
## 4 poo.trend 0.9974420 1 0.3179303
## ------
## --- GENE: rs2912771 ---
## ------- GxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 2.067427e-05 2 0.9999897
## 2 child 1.985742e-05 2 0.9999901
## 3 haplo.freq.trend 1.046453e-05 1 0.9974189
## 4 child.trend 1.046453e-05 1 0.9974189
## ------- PoOxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 2.010636e-05 2 0.9999899
## 2 poo 1.013049e-05 2 0.9999949
## 3 haplo.freq.trend 1.046235e-05 1 0.9974192
## 4 poo.trend 3.148643e-06 1 0.9985842
## ------
## --- GENE: rs1002246 ---
## ------- GxM: rs1002246
## gxe.test chisq df pval
## 1 haplo.freq 0.9690434 2 0.6159917
## 2 child 2.5465135 2 0.2799185
## 3 haplo.freq.trend 0.8964575 1 0.3437334
## 4 child.trend 2.4077841 1 0.1207332
## ------- PoOxM: rs1002246
## gxe.test chisq df pval
## 1 haplo.freq 2.10646107 2 0.3488091
## 2 poo 1.50698584 2 0.4707195
## 3 haplo.freq.trend 0.80074696 1 0.3708701
## 4 poo.trend 0.00956494 1 0.9220907
## ------
## --- GENE: rs7078160 ---
## ------- GxM: rs7078160
## gxe.test chisq df pval
## 1 haplo.freq 2.2976761 2 0.3170049
## 2 child 0.9955490 2 0.6078820
## 3 haplo.freq.trend 0.5405068 1 0.4622228
## 4 child.trend 0.5881063 1 0.4431523
## ------- PoOxM: rs7078160
## gxe.test chisq df pval
## 1 haplo.freq 4.50679044 2 0.1050420
## 2 poo 2.78075748 2 0.2489810
## 3 haplo.freq.trend 0.32439948 1 0.5689756
## 4 poo.trend 0.02753357 1 0.8682101
## ------
## --- GENE: rs4621895 ---
## ------- GxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 1.0923055 2 0.5791738
## 2 child 0.8416849 2 0.6564935
## 3 haplo.freq.trend 0.2458078 1 0.6200426
## 4 child.trend 0.2301242 1 0.6314317
## ------- PoOxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 1.3397265 2 0.5117786
## 2 poo 0.2211085 2 0.8953378
## 3 haplo.freq.trend 0.3629380 1 0.5468790
## 4 poo.trend 0.1067974 1 0.7438202
## ------
## --- GENE: rs470563 ---
## ------- GxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 5.855439 2 0.05351894
## 2 child 5.905385 2 0.05219897
## 3 haplo.freq.trend 1.235591 1 0.26632242
## 4 child.trend 1.206189 1 0.27208818
## ------- PoOxM: rs470563
## gxe.test chisq df pval
## 1 haplo.freq 4.7980050 2 0.09080849
## 2 poo 1.4457536 2 0.48535397
## 3 haplo.freq.trend 0.3508381 1 0.55363906
## 4 poo.trend 1.4280150 1 0.23208866
## ------
## --- GENE: rs3752075 ---
## ------- GxM: rs3752075
## gxe.test chisq df pval
## 1 haplo.freq 0.30429971 2 0.8588596
## 2 child 1.13000666 2 0.5683583
## 3 haplo.freq.trend 0.01086548 1 0.9169808
## 4 child.trend 0.16255449 1 0.6868155
## ------- PoOxM: rs3752075
## gxe.test chisq df pval
## 1 haplo.freq 4.676885 2 0.09647777
## 2 poo 5.161693 2 0.07570988
## 3 haplo.freq.trend 3.688091 1 0.05480232
## 4 poo.trend 5.148522 1 0.02326617
## ------## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## Warning: NAs in confidence intervals
## 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_ CLP .RData