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 CPO!
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,] 140 140 140 140 140 140 140 140 140 140 140
## [2,] 19 1 14 1 1 1 6 1 30 2 21
## PAX7 ABCA4 THADA 8q24 KIAA1598 SPRY2
## [1,] 140 140 140 140 140 140
## [2,] 1 6 1 1 1 1
## PAX7 ABCA4 IRF6 THADA FOXE1 KIAA1598 TPM1 MAFB
## [1,] 140 140 140 140 140 140 140 140
## [2,] 54 16 27 14 7 1 29 9
## Grouping limits, promoter regions:
## PAX7 ABCA4 IRF6 THADA 8q21.3
## 0% -0.97207216 -0.1263973 -0.9093316 -0.06637025 -0.04798853
## 33.33333% 0.04179234 0.9332765 0.1286800 0.95753457 0.96999621
## 66.66667% 0.04702266 0.9482500 0.1421482 0.96510975 0.97481086
## 100% 1.06486697 1.9760596 1.1823475 1.98202288 1.98465025
## 8q24 FOXE1 SPRY2 TPM1 NOG1
## 0% -0.6079150 -0.98833286 -0.04718125 -0.7844558 -0.5168446
## 33.33333% 0.7401398 0.01471336 0.97276755 0.2369365 0.5112204
## 66.66667% 0.8085185 0.01767373 0.97634393 0.2468472 0.5227991
## 100% 1.9000177 1.02904116 1.98448652 1.2699032 1.5623644
## MAFB
## 0% -0.94425691
## 33.33333% 0.07158662
## 66.66667% 0.07811642
## 100% 1.09978337
## Grouping limits, enhancer regions:
## PAX7 ABCA4 THADA 8q24 KIAA1598
## 0% -0.98203152 -0.0705633 -0.03593445 -0.05552524 -0.04927403
## 33.33333% 0.05098004 0.9447843 0.97554811 0.96646615 0.96952975
## 66.66667% 0.06191626 0.9504236 0.97832459 0.97083936 0.97435824
## 100% 1.09712359 1.9581093 1.98381519 1.98298609 1.98280388
## SPRY2
## 0% -0.2216691
## 33.33333% 0.8702008
## 66.66667% 0.8998556
## 100% 1.9656426
## Grouping limits, gene regions:
## PAX7 ABCA4 IRF6 THADA FOXE1
## 0% -0.8899276 -0.2474129 -0.5676986 -0.1473846 -0.94728559
## 33.33333% 0.1213945 0.7954831 0.4408043 0.8928109 0.07300903
## 66.66667% 0.1279799 0.8095066 0.4435408 0.9073640 0.08060211
## 100% 1.1419903 1.8258792 1.4536353 1.9371453 1.09678802
## KIAA1598 TPM1 MAFB
## 0% -0.04927403 -0.5298787 -0.96479317
## 33.33333% 0.96952975 0.4862132 0.04816014
## 66.66667% 0.97435824 0.4921662 0.05481327
## 100% 1.98280388 1.4984436 1.07717944
## 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: 2, 3, 16, 24, 28, 30 ... 616, 626, 628, 630, 637, 687
## INFO: Will select 140 rows and 72 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmpq6iF6H/ff4c44a7ad35.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 140 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd4397213bf.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/Rtmp84QCa6/ff1dd45b5c4d12.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd460f84c3f.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
## 47 46 47
##
## 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: ABCA4 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 140 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/Rtmp84QCa6/ff1dd435f2539b.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd432351084.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
## 47 46 47
##
## 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: IRF6 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 3
## INFO: Will select 140 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/Rtmp84QCa6/ff1dd450223fe1.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd435f727d8.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd433dc4d6b.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd46d787f53.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd47f354bb2.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd4147135e3.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
## 47 46 47
##
## 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: 8q24 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 6
## INFO: Will select 140 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/Rtmp84QCa6/ff1dd412e6ea2.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd4ba378c6.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd450ca2f1c.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd453523010.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd46a641b76.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd415c47b2b.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd43f5677fa.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd441c77d52.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd44beb4f63.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd435287a15.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd4278e1363.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd4773d41d9.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
## 47 46 47
##
## 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 0.552517 2 0.7586168
## 2 child 1.223059 2 0.5425206
## 3 haplo.freq.trend 0.532225 1 0.4656729
## 4 child.trend 1.056796 1 0.3039472
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 1.6502577 2 0.4381785
## 2 poo 3.5346300 2 0.1707909
## 3 haplo.freq.trend 0.1198006 1 0.7292508
## 4 poo.trend 0.1127348 1 0.7370518
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 1.07874371 2 0.5831144
## 2 child 1.33899077 2 0.5119669
## 3 haplo.freq.trend 0.01030729 1 0.9191339
## 4 child.trend 0.24983288 1 0.6171928
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 0.8783570 2 0.6445657
## 2 poo 1.1220531 2 0.5706230
## 3 haplo.freq.trend 0.1469312 1 0.7014854
## 4 poo.trend 0.6903610 1 0.4060416
## ------
## --- GENE: IRF6 ---
## ------- GxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 1.07489007 2 0.5842391
## 2 child 0.45206763 2 0.7976911
## 3 haplo.freq.trend 0.68885406 1 0.4065544
## 4 child.trend 0.01329454 1 0.9082058
## ------- PoOxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 1.65107598 2 0.4379993
## 2 poo 0.30879122 2 0.8569329
## 3 haplo.freq.trend 1.24505525 1 0.2644990
## 4 poo.trend 0.05210759 1 0.8194357
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 3.4800339 2 0.17551743
## 2 child 1.6557235 2 0.43698267
## 3 haplo.freq.trend 2.9403400 1 0.08639255
## 4 child.trend 0.8911589 1 0.34516345
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 4.221226 2 0.12116368
## 2 poo 2.299315 2 0.31674519
## 3 haplo.freq.trend 4.096926 1 0.04296126
## 4 poo.trend 1.058729 1 0.30350526
## ------
## --- GENE: 8q21.3 ---
## ------- GxM: 8q21.3
## gxe.test chisq df pval
## 1 haplo.freq 4.782568 2 0.09151211
## 2 child 5.778332 2 0.05562257
## 3 haplo.freq.trend 1.903722 1 0.16766232
## 4 child.trend 2.455138 1 0.11714084
## ------- PoOxM: 8q21.3
## gxe.test chisq df pval
## 1 haplo.freq 4.380747 2 0.11187493
## 2 poo 1.500751 2 0.47218915
## 3 haplo.freq.trend 3.362624 1 0.06669172
## 4 poo.trend 1.500153 1 0.22064779
## ------
## --- GENE: 8q24 ---
## ------- GxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 3.1904643 2 0.20286142
## 2 child 6.6744329 2 0.03553574
## 3 haplo.freq.trend 0.7231261 1 0.39512041
## 4 child.trend 3.4979801 1 0.06144373
## ------- PoOxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 2.9595545 2 0.2276884
## 2 poo 2.3487544 2 0.3090114
## 3 haplo.freq.trend 0.2295938 1 0.6318252
## 4 poo.trend 1.7876094 1 0.1812177
## ------
## --- GENE: FOXE1 ---
## ------- GxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.38699597 2 0.8240715
## 2 child 0.20265401 2 0.9036375
## 3 haplo.freq.trend 0.19066441 1 0.6623642
## 4 child.trend 0.08839096 1 0.7662328
## ------- PoOxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.91460103 2 0.6329901
## 2 poo 0.06908355 2 0.9660480
## 3 haplo.freq.trend 0.71648360 1 0.3972998
## 4 poo.trend 0.06797662 1 0.7943059
## ------
## --- GENE: SPRY2 ---
## ------- GxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 0.51946955 2 0.7712561
## 2 child 2.02757103 2 0.3628428
## 3 haplo.freq.trend 0.05513585 1 0.8143560
## 4 child.trend 0.47777042 1 0.4894340
## ------- PoOxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 1.61245034 2 0.4465405
## 2 poo 3.10053970 2 0.2121907
## 3 haplo.freq.trend 0.05079828 1 0.8216800
## 4 poo.trend 1.09997397 1 0.2942718
## ------
## --- GENE: TPM1 ---
## ------- GxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 3.6381836 2 0.16217297
## 2 child 0.3648299 2 0.83325550
## 3 haplo.freq.trend 3.6369216 1 0.05651133
## 4 child.trend 0.1299658 1 0.71846753
## ------- PoOxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 1.661537 2 0.4357143
## 2 poo 3.212308 2 0.2006579
## 3 haplo.freq.trend 1.532381 1 0.2157555
## 4 poo.trend 1.567559 1 0.2105619
## ------
## --- GENE: NOG1 ---
## ------- GxM: NOG1
## gxe.test chisq df pval
## 1 haplo.freq 2.17179152 2 0.3375992
## 2 child 4.12513931 2 0.1271269
## 3 haplo.freq.trend 0.04369637 1 0.8344195
## 4 child.trend 0.11231088 1 0.7375284
## ------- PoOxM: NOG1
## gxe.test chisq df pval
## 1 haplo.freq 3.935070512 2 0.1398010
## 2 poo 2.047559538 2 0.3592345
## 3 haplo.freq.trend 0.054573616 1 0.8152878
## 4 poo.trend 0.002728019 1 0.9583451
## ------
## --- GENE: MAFB ---
## ------- GxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 2.54140716 2 0.2806341
## 2 child 0.77640999 2 0.6782733
## 3 haplo.freq.trend 0.46653867 1 0.4945839
## 4 child.trend 0.08631949 1 0.7689094
## ------- PoOxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 3.115726 2 0.21058560
## 2 poo 7.439711 2 0.02423747
## 3 haplo.freq.trend 2.262965 1 0.13250018
## 4 poo.trend 5.002163 1 0.02531566
## ------
## 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: 2, 3, 16, 24, 28, 30 ... 616, 626, 628, 630, 637, 687
## INFO: Will select 140 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 140 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd435c6e55.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/Rtmp84QCa6/ff1dd4e55117c.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd479f33cdd.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
## 47 46 47
##
## 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: ABCA4 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 140 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/Rtmp84QCa6/ff1dd452fb4b6f.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd457c55328.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd452072512.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd432065e6a.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd442fc163.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd46f3c2b4c.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd43ca668f5.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd41e8f68ec.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd417913e6c.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd4764c2959.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
## 47 46 47
##
## 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 0.1436122 2 0.9307113
## 2 child 1.1699215 2 0.5571277
## 3 haplo.freq.trend 0.1230130 1 0.7257894
## 4 child.trend 0.4461441 1 0.5041718
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 0.6889633 2 0.70858756
## 2 poo 3.0201467 2 0.22089377
## 3 haplo.freq.trend 0.4359209 1 0.50909788
## 4 poo.trend 2.7859120 1 0.09509654
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 1.666297 2 0.4346786
## 2 child 1.735653 2 0.4198631
## 3 haplo.freq.trend 1.631242 1 0.2015313
## 4 child.trend 1.727564 1 0.1887222
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 1.3449591 2 0.5104413
## 2 poo 0.1175463 2 0.9429207
## 3 haplo.freq.trend 1.3304612 1 0.2487232
## 4 poo.trend 0.1161905 1 0.7332035
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.9830310 2 0.6116986
## 2 child 0.4806254 2 0.7863819
## 3 haplo.freq.trend 0.9491353 1 0.3299395
## 4 child.trend 0.4805224 1 0.4881858
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 1.994564 2 0.3688807
## 2 poo 2.799609 2 0.2466451
## 3 haplo.freq.trend 1.689673 1 0.1936441
## 4 poo.trend 1.897833 1 0.1683211
## ------
## --- GENE: 8q24 ---
## ------- GxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 0.9391814 2 0.6252581
## 2 child 0.2650521 2 0.8758801
## 3 haplo.freq.trend 0.2288815 1 0.6323544
## 4 child.trend 0.2257964 1 0.6346584
## ------- PoOxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 1.4214218 2 0.4912948
## 2 poo 3.4851184 2 0.1750718
## 3 haplo.freq.trend 0.1436669 1 0.7046625
## 4 poo.trend 0.1301552 1 0.7182712
## ------
## --- GENE: KIAA1598 ---
## ------- GxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.9019351 2 0.6370115
## 2 child 0.2960496 2 0.8624097
## 3 haplo.freq.trend 0.1143186 1 0.7352800
## 4 child.trend 0.1033893 1 0.7477996
## ------- PoOxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.3907932 2 0.8225084
## 2 poo 0.7405300 2 0.6905513
## 3 haplo.freq.trend 0.0132421 1 0.9083862
## 4 poo.trend 0.3201726 1 0.5715040
## ------
## --- GENE: SPRY2 ---
## ------- GxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 1.9653491 2 0.3743087
## 2 child 1.4308976 2 0.4889726
## 3 haplo.freq.trend 0.4138210 1 0.5200364
## 4 child.trend 0.2921039 1 0.5888754
## ------- PoOxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 2.46473056 2 0.2916020
## 2 poo 2.47262993 2 0.2904526
## 3 haplo.freq.trend 0.01489719 1 0.9028562
## 4 poo.trend 2.33231994 1 0.1267129
## ------
## 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: 2, 3, 16, 24, 28, 30 ... 616, 626, 628, 630, 637, 687
## INFO: Will select 140 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 140 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd462633219.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/Rtmp84QCa6/ff1dd41f825e11.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd45f0e4106.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
## 47 46 47
##
## 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: ABCA4 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 140 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/Rtmp84QCa6/ff1dd46a9b2d05.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd429db7e62.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
## 47 46 47
##
## 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: IRF6 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 3
## INFO: Will select 140 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/Rtmp84QCa6/ff1dd46b7f1a3d.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd433c02ddc.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd42cfd28f2.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd462141d4.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd46cc66615.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd475aa2e3b.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd41f270c9.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd44c71d17.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd4537b52e4.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd4562b7302.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
## 47 46 47
##
## 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 140 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/Rtmp84QCa6/ff1dd45ec12971.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
## 47 46 47
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmp84QCa6/ff1dd42f4a23ab.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
## 47 46 47
##
## 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 1.362442 2 0.5059988
## 2 child 1.435372 2 0.4878798
## 3 haplo.freq.trend 1.006791 1 0.3156729
## 4 child.trend 1.259596 1 0.2617276
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 1.13792153 2 0.5661135
## 2 poo 0.40495683 2 0.8167041
## 3 haplo.freq.trend 0.38478164 1 0.5350552
## 4 poo.trend 0.07553805 1 0.7834377
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 0.3389508692 2 0.8441075
## 2 child 1.9754411562 2 0.3724246
## 3 haplo.freq.trend 0.0003493806 1 0.9850870
## 4 child.trend 1.8911380933 1 0.1690736
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 0.22529760 2 0.8934644
## 2 poo 0.43751069 2 0.8035183
## 3 haplo.freq.trend 0.02989577 1 0.8627269
## 4 poo.trend 0.16459543 1 0.6849604
## ------
## --- GENE: IRF6 ---
## ------- GxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 0.238486137 2 0.8875920
## 2 child 0.034978841 2 0.9826626
## 3 haplo.freq.trend 0.035564356 1 0.8504180
## 4 child.trend 0.006885951 1 0.9338661
## ------- PoOxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 0.213641092 2 0.8986869
## 2 poo 0.215706288 2 0.8977594
## 3 haplo.freq.trend 0.042976540 1 0.8357695
## 4 poo.trend 0.006449918 1 0.9359896
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.8907557 2 0.6405822
## 2 child 0.3730312 2 0.8298456
## 3 haplo.freq.trend 0.4260462 1 0.5139354
## 4 child.trend 0.1384109 1 0.7098659
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 1.2597721 2 0.5326525
## 2 poo 4.1887977 2 0.1231442
## 3 haplo.freq.trend 0.0402164 1 0.8410581
## 4 poo.trend 1.6295334 1 0.2017676
## ------
## --- GENE: FOXE1 ---
## ------- GxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.38753930 2 0.82384765
## 2 child 5.14190460 2 0.07646270
## 3 haplo.freq.trend 0.05000506 1 0.82305447
## 4 child.trend 4.93002777 1 0.02639389
## ------- PoOxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.5444150 2 0.7616962
## 2 poo 2.9369465 2 0.2302768
## 3 haplo.freq.trend 0.5319249 1 0.4657987
## 4 poo.trend 2.5522507 1 0.1101373
## ------
## --- GENE: KIAA1598 ---
## ------- GxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.9019351 2 0.6370115
## 2 child 0.2960496 2 0.8624097
## 3 haplo.freq.trend 0.1143186 1 0.7352800
## 4 child.trend 0.1033893 1 0.7477996
## ------- PoOxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.3907932 2 0.8225084
## 2 poo 0.7405300 2 0.6905513
## 3 haplo.freq.trend 0.0132421 1 0.9083862
## 4 poo.trend 0.3201726 1 0.5715040
## ------
## --- GENE: TPM1 ---
## ------- GxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 0.43629136 2 0.8040083
## 2 child 0.55513033 2 0.7576262
## 3 haplo.freq.trend 0.43614668 1 0.5089882
## 4 child.trend 0.02657381 1 0.8705068
## ------- PoOxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 0.05069073 2 0.9749731
## 2 poo 0.72045501 2 0.6975176
## 3 haplo.freq.trend 0.05069025 1 0.8218665
## 4 poo.trend 0.64529633 1 0.4217994
## ------
## --- GENE: MAFB ---
## ------- GxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 7.3317710 2 0.02558151
## 2 child 1.5556468 2 0.45940485
## 3 haplo.freq.trend 2.2264666 1 0.13566378
## 4 child.trend 0.4425119 1 0.50591254
## ------- PoOxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 9.293180 2 0.00959426
## 2 poo 3.992279 2 0.13585876
## 3 haplo.freq.trend 3.651988 1 0.05600231
## 4 poo.trend 3.552776 1 0.05944591
## ------
## Saved image to file: GxM_PoOxM_new_betas_mult_ CPO .RData