I chose those SNPs (from Moreno et al., 2017):
## Chr snpname pos1 pos2 gene_name
## 1 1 rs742071 18979874 18979875 PAX7
## 2 1 rs560426 94553438 94553439 ABCA4
## 3 1 rs642961 209989270 209989271 IRF6
## 4 2 rs7590268 43540125 43540126 THADA
## 5 8 rs12543318 88868340 88868341 8q21.3
## 6 8 rs987525 129946154 129946155 8q24
## 7 9 rs3758249 100614140 100614141 FOXE1
## 8 10 rs7078160 118827560 118827561 KIAA1598
## 9 13 rs8001641 80692811 80692812 SPRY2
## 10 15 rs1873147 63312632 63312633 TPM1
## 11 17 rs227731 54773238 54773239 NOG1
## 12 20 rs13041247 39269074 39269075 MAFB
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:
## PAX7 ABCA4 IRF6 THADA 8q21.3 8q24 FOXE1 SPRY2 TPM1 NOG1 MAFB
## [1,] 456 456 456 456 456 456 456 456 456 456 456
## [2,] 19 1 14 1 1 1 6 1 30 2 21
## PAX7 ABCA4 THADA 8q24 KIAA1598 SPRY2
## [1,] 456 456 456 456 456 456
## [2,] 1 6 1 1 1 1
## PAX7 ABCA4 IRF6 THADA FOXE1 KIAA1598 TPM1 MAFB
## [1,] 456 456 456 456 456 456 456 456
## [2,] 54 16 27 14 7 1 29 9
## Grouping limits, promoter regions:
## PAX7 ABCA4 IRF6 THADA 8q21.3
## 0% -0.96761470 -0.1226563 -0.9070420 -0.07568628 -0.04982769
## 33.33333% 0.04107762 0.9305160 0.1239632 0.95861852 0.97059055
## 66.66667% 0.04505021 0.9435014 0.1382401 0.96643829 0.97453809
## 100% 1.05945242 1.9725180 1.1890123 1.98399919 1.98797095
## 8q24 FOXE1 SPRY2 TPM1 NOG1
## 0% -0.6064441 -0.98980591 -0.04921919 -0.7871518 -0.5163544
## 33.33333% 0.7649811 0.01529739 0.97252389 0.2364870 0.5115287
## 66.66667% 0.8186856 0.01790384 0.97689237 0.2471763 0.5219291
## 100% 1.9279907 1.03072341 1.98681766 1.2732165 1.5568729
## MAFB
## 0% -0.94988804
## 33.33333% 0.07007318
## 66.66667% 0.07757347
## 100% 1.09951486
## Grouping limits, enhancer regions:
## PAX7 ABCA4 THADA 8q24 KIAA1598
## 0% -0.97800966 -0.06947673 -0.03856665 -0.05647725 -0.05331135
## 33.33333% 0.05031837 0.94650544 0.97543222 0.96794589 0.96960934
## 66.66667% 0.06322431 0.95053744 0.97841074 0.97227496 0.97427821
## 100% 1.10677580 1.96230521 1.98474139 1.98483253 1.98548174
## SPRY2
## 0% -0.2760715
## 33.33333% 0.8637778
## 66.66667% 0.8988084
## 100% 1.9626595
## Grouping limits, gene regions:
## PAX7 ABCA4 IRF6 THADA FOXE1
## 0% -0.8973680 -0.2535997 -0.5694463 -0.1495130 -0.95107472
## 33.33333% 0.1210821 0.7954842 0.4394528 0.8935318 0.07307813
## 66.66667% 0.1264642 0.8078129 0.4434949 0.9068246 0.08190111
## 100% 1.1423740 1.8255052 1.4521884 1.9430708 1.10499976
## KIAA1598 TPM1 MAFB
## 0% -0.05331135 -0.5300076 -0.96638997
## 33.33333% 0.96960934 0.4877754 0.04743475
## 66.66667% 0.97427821 0.4926808 0.05394421
## 100% 1.98548174 1.5009216 1.07822984
## 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 72 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmpq6iF6H/ff4c43ff22ad9.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: PAX7 is in position: 1
## SNP for gene: ABCA4 is in position: 2
## SNP for gene: IRF6 is in position: 3
## SNP for gene: THADA is in position: 4
## SNP for gene: 8q21.3 is in position: 5
## SNP for gene: 8q24 is in position: 6
## SNP for gene: FOXE1 is in position: 7
## SNP for gene: SPRY2 is in position: 9
## SNP for gene: TPM1 is in position: 10
## SNP for gene: NOG1 is in position: 11
## SNP for gene: MAFB is in position: 12
##
## HaplinStrat:
## === GENE: PAX7 ===
## 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/RtmpWQ6WYo/ff1124b632f92.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/RtmpWQ6WYo/ff112469c776ff.ff
## ...done, all alleles: G 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/RtmpWQ6WYo/ff112479e537ad.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"...
## 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
## === GENE: ABCA4 ===
## 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/RtmpWQ6WYo/ff112473df325f.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/RtmpWQ6WYo/ff11241b5f5a06.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: IRF6 ===
## 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_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/RtmpWQ6WYo/ff112444065cc2.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/RtmpWQ6WYo/ff11244f02053.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: THADA ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 4
## 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/RtmpWQ6WYo/ff11245a5f245.ff
## ...done, all alleles: G 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/RtmpWQ6WYo/ff11243c302e37.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: 8q21.3 ===
## 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/RtmpWQ6WYo/ff112476705f3c.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/RtmpWQ6WYo/ff11242a7f4b68.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: 8q24 ===
## 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/RtmpWQ6WYo/ff11244da478ae.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/RtmpWQ6WYo/ff11244f7e2830.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: FOXE1 ===
## 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/RtmpWQ6WYo/ff112451c94d6.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/RtmpWQ6WYo/ff112439171ec.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: SPRY2 ===
## 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/RtmpWQ6WYo/ff112479323a4.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/RtmpWQ6WYo/ff11244a643790.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: TPM1 ===
## 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/RtmpWQ6WYo/ff11246d16673a.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/RtmpWQ6WYo/ff112435631e20.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: NOG1 ===
## 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_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/RtmpWQ6WYo/ff1124704f2c70.ff
## ...done, all alleles: G 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/RtmpWQ6WYo/ff112456406538.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: MAFB ===
## 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/RtmpWQ6WYo/ff1124759c4350.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/RtmpWQ6WYo/ff112441703b86.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: PAX7 ---
## ------- GxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 1.11961920 2 0.5713178
## 2 child 0.65706133 2 0.7199808
## 3 haplo.freq.trend 0.04862627 1 0.8254711
## 4 child.trend 0.52214708 1 0.4699272
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 0.14380991 2 0.9306193
## 2 poo 1.80209425 2 0.4061442
## 3 haplo.freq.trend 0.13162899 1 0.7167490
## 4 poo.trend 0.05403629 1 0.8161830
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 0.8062419 2 0.6682313
## 2 child 0.3631155 2 0.8339701
## 3 haplo.freq.trend 0.3662665 1 0.5450464
## 4 child.trend 0.2941349 1 0.5875829
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 2.1340439 2 0.3440315
## 2 poo 4.5269862 2 0.1039866
## 3 haplo.freq.trend 0.1762889 1 0.6745821
## 4 poo.trend 1.0570531 1 0.3038883
## ------
## --- GENE: IRF6 ---
## ------- GxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 0.67250162 2 0.7144439
## 2 child 4.18357274 2 0.1234664
## 3 haplo.freq.trend 0.04469822 1 0.8325599
## 4 child.trend 0.05386932 1 0.8164622
## ------- PoOxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 1.441583 2 0.4863672
## 2 poo 1.899327 2 0.3868711
## 3 haplo.freq.trend 0.474292 1 0.4910192
## 4 poo.trend 1.544278 1 0.2139821
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 3.574275 2 0.1674388
## 2 child 1.235680 2 0.5391078
## 3 haplo.freq.trend 3.570260 1 0.0588231
## 4 child.trend 1.225024 1 0.2683769
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 3.134592 2 0.20860847
## 2 poo 1.442241 2 0.48620725
## 3 haplo.freq.trend 2.927319 1 0.08709201
## 4 poo.trend 0.201141 1 0.65380141
## ------
## --- GENE: 8q21.3 ---
## ------- GxM: 8q21.3
## gxe.test chisq df pval
## 1 haplo.freq 3.054216 2 0.2171628
## 2 child 3.843559 2 0.1463463
## 3 haplo.freq.trend 2.370291 1 0.1236640
## 4 child.trend 2.444208 1 0.1179594
## ------- PoOxM: 8q21.3
## gxe.test chisq df pval
## 1 haplo.freq 0.078518020 2 0.961501638
## 2 poo 10.385590548 2 0.005556453
## 3 haplo.freq.trend 0.006923299 1 0.933687455
## 4 poo.trend 9.563924590 1 0.001984384
## ------
## --- GENE: 8q24 ---
## ------- GxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 1.822166 2 0.40208847
## 2 child 6.081716 2 0.04779387
## 3 haplo.freq.trend 1.087565 1 0.29701139
## 4 child.trend 5.468428 1 0.01936303
## ------- PoOxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 0.299561922 2 0.86089653
## 2 poo 5.049425100 2 0.08008133
## 3 haplo.freq.trend 0.271081458 1 0.60260724
## 4 poo.trend 0.000746468 1 0.97820326
## ------
## --- GENE: FOXE1 ---
## ------- GxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 1.44312127 2 0.4859932
## 2 child 1.05515913 2 0.5900314
## 3 haplo.freq.trend 0.24195045 1 0.6228009
## 4 child.trend 0.06178114 1 0.8037026
## ------- PoOxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.23036365 2 0.8912041
## 2 poo 0.99060286 2 0.6093872
## 3 haplo.freq.trend 0.07148505 1 0.7891867
## 4 poo.trend 0.13796051 1 0.7103170
## ------
## --- GENE: SPRY2 ---
## ------- GxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 3.10714302 2 0.2114913
## 2 child 2.27184759 2 0.3211253
## 3 haplo.freq.trend 0.11899724 1 0.7301246
## 4 child.trend 0.03925592 1 0.8429425
## ------- PoOxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 1.39094562 2 0.4988385
## 2 poo 0.92140662 2 0.6308398
## 3 haplo.freq.trend 0.01984801 1 0.8879624
## 4 poo.trend 0.13418771 1 0.7141290
## ------
## --- GENE: TPM1 ---
## ------- GxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 5.829611 2 5.421458e-02
## 2 child 19.580397 2 5.599778e-05
## 3 haplo.freq.trend 5.829596 1 1.575874e-02
## 4 child.trend 19.176562 1 1.191676e-05
## ------- PoOxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 4.9268832742 2 0.08514142
## 2 poo 0.1868720655 2 0.91079628
## 3 haplo.freq.trend 4.8351082516 1 0.02788589
## 4 poo.trend 0.0002033524 1 0.98862242
## ------
## --- GENE: NOG1 ---
## ------- GxM: NOG1
## gxe.test chisq df pval
## 1 haplo.freq 2.1957697 2 0.3335759
## 2 child 1.1103931 2 0.5739594
## 3 haplo.freq.trend 2.1920611 1 0.1387236
## 4 child.trend 0.2780459 1 0.5979849
## ------- PoOxM: NOG1
## gxe.test chisq df pval
## 1 haplo.freq 2.6487650 2 0.2659671
## 2 poo 1.4398203 2 0.4867960
## 3 haplo.freq.trend 2.1919671 1 0.1387320
## 4 poo.trend 0.3234408 1 0.5695472
## ------
## --- GENE: MAFB ---
## ------- GxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 3.03853340 2 0.2188723
## 2 child 2.58307269 2 0.2748482
## 3 haplo.freq.trend 0.50563031 1 0.4770366
## 4 child.trend 0.03044801 1 0.8614776
## ------- PoOxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 1.9749189501 2 0.3725219
## 2 poo 0.0449746255 2 0.9777636
## 3 haplo.freq.trend 0.4186108605 1 0.5176310
## 4 poo.trend 0.0003809158 1 0.9844286
## ------
## 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 72 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: PAX7 is in position: 1
## SNP for gene: ABCA4 is in position: 2
## SNP for gene: THADA is in position: 4
## SNP for gene: 8q24 is in position: 6
## SNP for gene: KIAA1598 is in position: 8
## SNP for gene: SPRY2 is in position: 9
##
## HaplinStrat:
## === GENE: PAX7 ===
## 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/RtmpWQ6WYo/ff112420af634b.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/RtmpWQ6WYo/ff112430953e9c.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/RtmpWQ6WYo/ff1124104e399a.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: ABCA4 ===
## 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_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/RtmpWQ6WYo/ff112454a2388b.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/RtmpWQ6WYo/ff11242ad6e17.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"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
## === GENE: THADA ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 4
## 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/RtmpWQ6WYo/ff112458bb61b3.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/RtmpWQ6WYo/ff11247a2d3d80.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: 8q24 ===
## 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_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/RtmpWQ6WYo/ff11241287b7a.ff
## ...done, all alleles: A C
## ...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/RtmpWQ6WYo/ff1124294a2058.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: KIAA1598 ===
## 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/RtmpWQ6WYo/ff112416b5b1e.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/RtmpWQ6WYo/ff11241f0715d8.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"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
## === GENE: SPRY2 ===
## 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_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/RtmpWQ6WYo/ff11241131762d.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/RtmpWQ6WYo/ff11244a32c68.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: PAX7 ---
## ------- GxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 0.3682165 2 0.8318458
## 2 child 1.0381979 2 0.5950565
## 3 haplo.freq.trend 0.3580632 1 0.5495839
## 4 child.trend 1.0359689 1 0.3087609
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 0.52193967 2 0.7703042
## 2 poo 0.44032983 2 0.8023865
## 3 haplo.freq.trend 0.20491258 1 0.6507844
## 4 poo.trend 0.01602826 1 0.8992548
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 1.0561282 2 0.5897456
## 2 child 3.7243061 2 0.1553378
## 3 haplo.freq.trend 0.6113612 1 0.4342758
## 4 child.trend 0.4036841 1 0.5251927
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 5.909523 2 0.05209109
## 2 poo 7.107895 2 0.02861147
## 3 haplo.freq.trend 2.484328 1 0.11498542
## 4 poo.trend 2.099940 1 0.14730496
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.3590373 2 0.8356724
## 2 child 0.3305864 2 0.8476451
## 3 haplo.freq.trend 0.3528133 1 0.5525249
## 4 child.trend 0.1694911 1 0.6805645
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.9114594 2 0.6339852
## 2 poo 1.3384644 2 0.5121016
## 3 haplo.freq.trend 0.8208560 1 0.3649300
## 4 poo.trend 0.4322709 1 0.5108767
## ------
## --- GENE: 8q24 ---
## ------- GxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 3.4312672 2 0.1798497
## 2 child 3.0163797 2 0.2213102
## 3 haplo.freq.trend 2.1416011 1 0.1433522
## 4 child.trend 0.9333087 1 0.3340046
## ------- PoOxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 2.5094881 2 0.2851488
## 2 poo 0.6240274 2 0.7319715
## 3 haplo.freq.trend 1.1360061 1 0.2864978
## 4 poo.trend 0.4848454 1 0.4862357
## ------
## --- GENE: KIAA1598 ---
## ------- GxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.7956454 2 0.6717811
## 2 child 2.7368454 2 0.2545081
## 3 haplo.freq.trend 0.2459670 1 0.6199293
## 4 child.trend 2.0820268 1 0.1490422
## ------- PoOxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.7096362 2 0.7013010
## 2 poo 0.2447960 2 0.8847962
## 3 haplo.freq.trend 0.3935541 1 0.5304371
## 4 poo.trend 0.2015582 1 0.6534660
## ------
## --- GENE: SPRY2 ---
## ------- GxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 0.09224743 2 0.9549238
## 2 child 0.34395530 2 0.8419980
## 3 haplo.freq.trend 0.04293242 1 0.8358526
## 4 child.trend 0.29568242 1 0.5866019
## ------- PoOxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 0.02910022 2 0.9855552
## 2 poo 1.32625305 2 0.5152379
## 3 haplo.freq.trend 0.01017967 1 0.9196343
## 4 poo.trend 0.02392163 1 0.8770845
## ------
## 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 72 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: PAX7 is in position: 1
## SNP for gene: ABCA4 is in position: 2
## SNP for gene: IRF6 is in position: 3
## SNP for gene: THADA is in position: 4
## SNP for gene: FOXE1 is in position: 7
## SNP for gene: KIAA1598 is in position: 8
## SNP for gene: TPM1 is in position: 10
## SNP for gene: MAFB is in position: 12
##
## HaplinStrat:
## === GENE: PAX7 ===
## 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/RtmpWQ6WYo/ff11245c401a2a.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/RtmpWQ6WYo/ff112426155a77.ff
## ...done, all alleles: G 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/RtmpWQ6WYo/ff1124495d731.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"...
## 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: ABCA4 ===
## 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_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/RtmpWQ6WYo/ff11244d776ea1.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/RtmpWQ6WYo/ff112455c21878.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: IRF6 ===
## 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/RtmpWQ6WYo/ff112426f77c5d.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/RtmpWQ6WYo/ff112426d57617.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: THADA ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 4
## 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/RtmpWQ6WYo/ff11248f8105f.ff
## ...done, all alleles: G 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/RtmpWQ6WYo/ff112468c03ed4.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: FOXE1 ===
## 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_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/RtmpWQ6WYo/ff112443fc2952.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/RtmpWQ6WYo/ff1124782e714d.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: KIAA1598 ===
## 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/RtmpWQ6WYo/ff1124112e6852.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/RtmpWQ6WYo/ff1124ccd871.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"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
## === GENE: TPM1 ===
## 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_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/RtmpWQ6WYo/ff112410d9116f.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/RtmpWQ6WYo/ff112473d36804.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: MAFB ===
## 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_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/RtmpWQ6WYo/ff112458ee5c30.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/RtmpWQ6WYo/ff11245a76191e.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: PAX7 ---
## ------- GxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 2.5460365 2 0.2799853
## 2 child 2.1955035 2 0.3336203
## 3 haplo.freq.trend 0.4534065 1 0.5007217
## 4 child.trend 0.3147476 1 0.5747814
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 2.1326756120 2 0.3442670
## 2 poo 0.8417947832 2 0.6564575
## 3 haplo.freq.trend 0.0001065571 1 0.9917639
## 4 poo.trend 0.6074390079 1 0.4357537
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 2.2061669 2 0.33184627
## 2 child 7.0151618 2 0.02996933
## 3 haplo.freq.trend 0.0280637 1 0.86695915
## 4 child.trend 3.9497872 1 0.04687730
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 7.573366923 2 0.02267067
## 2 poo 7.187839809 2 0.02749036
## 3 haplo.freq.trend 0.001336625 1 0.97083593
## 4 poo.trend 0.165865306 1 0.68381289
## ------
## --- GENE: IRF6 ---
## ------- GxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 5.1077805 2 0.0777785
## 2 child 1.9284475 2 0.3812790
## 3 haplo.freq.trend 2.3092740 1 0.1286041
## 4 child.trend 0.1055703 1 0.7452448
## ------- PoOxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 6.7251830 2 0.03464536
## 2 poo 1.5635706 2 0.45758834
## 3 haplo.freq.trend 3.0065744 1 0.08292738
## 4 poo.trend 0.5031747 1 0.47810849
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.146567911 2 0.9293369
## 2 child 1.562251175 2 0.4578903
## 3 haplo.freq.trend 0.000238673 1 0.9876739
## 4 child.trend 0.223520965 1 0.6363701
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.025678514 2 0.9872428
## 2 poo 1.866416885 2 0.3932898
## 3 haplo.freq.trend 0.004985763 1 0.9437082
## 4 poo.trend 0.003056205 1 0.9559130
## ------
## --- GENE: FOXE1 ---
## ------- GxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.6382512 2 7.267843e-01
## 2 child 18.7241053 2 8.592355e-05
## 3 haplo.freq.trend 0.3071309 1 5.794461e-01
## 4 child.trend 15.3947460 1 8.723050e-05
## ------- PoOxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 1.1468354 2 0.5635959
## 2 poo 1.1157830 2 0.5724147
## 3 haplo.freq.trend 1.1211368 1 0.2896738
## 4 poo.trend 0.6391222 1 0.4240288
## ------
## --- GENE: KIAA1598 ---
## ------- GxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.7956454 2 0.6717811
## 2 child 2.7368454 2 0.2545081
## 3 haplo.freq.trend 0.2459670 1 0.6199293
## 4 child.trend 2.0820268 1 0.1490422
## ------- PoOxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.7096362 2 0.7013010
## 2 poo 0.2447960 2 0.8847962
## 3 haplo.freq.trend 0.3935541 1 0.5304371
## 4 poo.trend 0.2015582 1 0.6534660
## ------
## --- GENE: TPM1 ---
## ------- GxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 2.895683 2 0.2350772
## 2 child 1.787032 2 0.4092145
## 3 haplo.freq.trend 2.158417 1 0.1417907
## 4 child.trend 1.772083 1 0.1831245
## ------- PoOxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 4.12914723 2 0.1268724
## 2 poo 3.26695516 2 0.1952494
## 3 haplo.freq.trend 1.45662170 1 0.2274684
## 4 poo.trend 0.00221983 1 0.9624215
## ------
## --- GENE: MAFB ---
## ------- GxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 1.2306131 2 0.5404752
## 2 child 0.2565031 2 0.8796321
## 3 haplo.freq.trend 1.1346038 1 0.2867955
## 4 child.trend 0.2523384 1 0.6154333
## ------- PoOxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 1.38137131 2 0.5012323
## 2 poo 1.26650539 2 0.5308623
## 3 haplo.freq.trend 1.35130826 1 0.2450495
## 4 poo.trend 0.03283211 1 0.8562135
## ------
## Saved image to file: GxM_PoOxM_new_betas_mult_ cntrl .RData