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 CLO!
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,] 103 103 103 103 103 103 103 103 103 103 103
## [2,] 19 1 14 1 1 1 6 1 30 2 21
## PAX7 ABCA4 THADA 8q24 KIAA1598 SPRY2
## [1,] 103 103 103 103 103 103
## [2,] 1 6 1 1 1 1
## PAX7 ABCA4 IRF6 THADA FOXE1 KIAA1598 TPM1 MAFB
## [1,] 103 103 103 103 103 103 103 103
## [2,] 54 16 27 14 7 1 29 9
## Grouping limits, promoter regions:
## PAX7 ABCA4 IRF6 THADA 8q21.3
## 0% -0.96679087 -0.1076969 -0.8951868 -0.07298237 -0.04989332
## 33.33333% 0.04092677 0.9318756 0.1217083 0.95793384 0.97208768
## 66.66667% 0.04615895 0.9444262 0.1381032 0.96591312 0.97557968
## 100% 1.06021570 1.9650323 1.1835425 1.97900957 1.98227459
## 8q24 FOXE1 SPRY2 TPM1 NOG1
## 0% -0.5867750 -0.98812215 -0.04906648 -0.7922317 -0.5109943
## 33.33333% 0.7827141 0.01487625 0.97143674 0.2354813 0.5119662
## 66.66667% 0.8306022 0.01773309 0.97745383 0.2446527 0.5215875
## 100% 1.9242244 1.03050833 1.98409009 1.2595121 1.5606337
## MAFB
## 0% -0.94418914
## 33.33333% 0.07206218
## 66.66667% 0.07898675
## 100% 1.10393818
## Grouping limits, enhancer regions:
## PAX7 ABCA4 THADA 8q24 KIAA1598
## 0% -0.97485797 -0.07028522 -0.03692979 -0.05521512 -0.05330819
## 33.33333% 0.04945834 0.94556827 0.97623080 0.96768343 0.97113746
## 66.66667% 0.06098747 0.95041462 0.97896218 0.97159743 0.97519898
## 100% 1.08631443 1.96131206 1.98866802 1.98308790 1.98022485
## SPRY2
## 0% -0.2299239
## 33.33333% 0.8649228
## 66.66667% 0.8937523
## 100% 1.9405975
## Grouping limits, gene regions:
## PAX7 ABCA4 IRF6 THADA FOXE1
## 0% -0.8876057 -0.2437876 -0.5677786 -0.1356056 -0.94081032
## 33.33333% 0.1212373 0.8002205 0.4401858 0.8947467 0.07461174
## 66.66667% 0.1275778 0.8086263 0.4433498 0.9064302 0.08447336
## 100% 1.1438084 1.8282649 1.4536303 1.9330904 1.10090361
## KIAA1598 TPM1 MAFB
## 0% -0.05330819 -0.5319530 -0.96271565
## 33.33333% 0.97113746 0.4862428 0.04818571
## 66.66667% 0.97519898 0.4920519 0.05491350
## 100% 1.98022485 1.5006847 1.07930891
## 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: 11, 23, 27, 47, 56, 70 ... 666, 668, 669, 674, 676, 678
## INFO: Will select 103 rows and 72 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmpq6iF6H/ff4c423697037.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 103 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff2080206a2359.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/RtmpeWvLZW/ff2080679d2b61.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20803af27502.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff20803f367e38.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff208043556af3.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff208039af11bb.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20807bf45fe7.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff208026a12e2.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20805eddc03.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff20802e1b128.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff2080286e4153.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff2080111b390d.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20803dc3246.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff20803a194e94.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20807ae482d.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff20801d7c67c5.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20802429c1.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff20806a23472b.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20801648119a.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff20809de7657.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff2080274214b8.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff208071f25c.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff2080160a78fe.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
## 35 34 34
##
## 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 2.035711547 2 0.36136897
## 2 child 5.497728956 2 0.06400049
## 3 haplo.freq.trend 0.008922983 1 0.92474253
## 4 child.trend 0.013526887 1 0.90741071
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 1.4827246 2 0.4764644
## 2 poo 0.1522194 2 0.9267145
## 3 haplo.freq.trend 0.1434599 1 0.7048654
## 4 poo.trend 0.1400367 1 0.7082445
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 0.8961878 2 0.6388447
## 2 child 1.6970095 2 0.4280545
## 3 haplo.freq.trend 0.3703381 1 0.5428200
## 4 child.trend 0.9449855 1 0.3309990
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 1.46950406 2 0.4796244
## 2 poo 0.67073099 2 0.7150767
## 3 haplo.freq.trend 0.01928019 1 0.8895662
## 4 poo.trend 0.37755524 1 0.5389145
## ------
## --- GENE: IRF6 ---
## ------- GxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 0.37064835 2 0.8308349
## 2 child 1.18333682 2 0.5534032
## 3 haplo.freq.trend 0.18783805 1 0.6647221
## 4 child.trend 0.09465301 1 0.7583431
## ------- PoOxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 2.6279422 2 0.2687507
## 2 poo 4.5301963 2 0.1038198
## 3 haplo.freq.trend 0.7306665 1 0.3926672
## 4 poo.trend 2.2503396 1 0.1335851
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 2.279425 2 0.3199110
## 2 child 3.506525 2 0.1732079
## 3 haplo.freq.trend 1.508453 1 0.2193753
## 4 child.trend 3.252571 1 0.0713115
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 3.684859 2 0.1584321
## 2 poo 1.020076 2 0.6004727
## 3 haplo.freq.trend 2.545119 1 0.1106356
## 4 poo.trend 1.019608 1 0.3126119
## ------
## --- GENE: 8q21.3 ---
## ------- GxM: 8q21.3
## gxe.test chisq df pval
## 1 haplo.freq 2.11958111 2 0.3465284
## 2 child 2.25821946 2 0.3233210
## 3 haplo.freq.trend 0.05718163 1 0.8110073
## 4 child.trend 0.06936856 1 0.7922584
## ------- PoOxM: 8q21.3
## gxe.test chisq df pval
## 1 haplo.freq 5.8023704 2 0.05495804
## 2 poo 7.4361597 2 0.02428055
## 3 haplo.freq.trend 0.0666494 1 0.79627922
## 4 poo.trend 0.2437207 1 0.62153168
## ------
## --- GENE: 8q24 ---
## ------- GxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 2.1752748 2 0.3370118
## 2 child 1.6879768 2 0.4299921
## 3 haplo.freq.trend 1.0158923 1 0.3134954
## 4 child.trend 0.6503701 1 0.4199804
## ------- PoOxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 2.683930 2 0.26133161
## 2 poo 4.886916 2 0.08685998
## 3 haplo.freq.trend 2.263888 1 0.13242126
## 4 poo.trend 4.066379 1 0.04374494
## ------
## --- GENE: FOXE1 ---
## ------- GxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.0268230829 2 0.9866780
## 2 child 0.2624073167 2 0.8770391
## 3 haplo.freq.trend 0.0001379107 1 0.9906302
## 4 child.trend 0.2548753595 1 0.6136629
## ------- PoOxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.4103043 2 0.8145234
## 2 poo 0.9661735 2 0.6168763
## 3 haplo.freq.trend 0.2446056 1 0.6208993
## 4 poo.trend 0.9581612 1 0.3276506
## ------
## --- GENE: SPRY2 ---
## ------- GxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 0.6576839 2 0.7197568
## 2 child 1.2540718 2 0.5341728
## 3 haplo.freq.trend 0.6415647 1 0.4231448
## 4 child.trend 0.4893535 1 0.4842158
## ------- PoOxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 2.446811 2 0.2942265
## 2 poo 3.795700 2 0.1498905
## 3 haplo.freq.trend 1.395158 1 0.2375360
## 4 poo.trend 0.830976 1 0.3619905
## ------
## --- GENE: TPM1 ---
## ------- GxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 1.648393 2 0.4385873
## 2 child 1.844377 2 0.3976478
## 3 haplo.freq.trend 1.212435 1 0.2708504
## 4 child.trend 1.700014 1 0.1922861
## ------- PoOxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 2.6498563910 2 0.2658220
## 2 poo 2.2625645887 2 0.3226193
## 3 haplo.freq.trend 1.0824623604 1 0.2981474
## 4 poo.trend 0.0002185029 1 0.9882062
## ------
## --- GENE: NOG1 ---
## ------- GxM: NOG1
## gxe.test chisq df pval
## 1 haplo.freq 0.3746052 2 0.8291928
## 2 child 0.1236835 2 0.9400316
## 3 haplo.freq.trend 0.1794274 1 0.6718658
## 4 child.trend 0.0980962 1 0.7541263
## ------- PoOxM: NOG1
## gxe.test chisq df pval
## 1 haplo.freq 1.336862 2 0.51251218
## 2 poo 8.856252 2 0.01193684
## 3 haplo.freq.trend 1.035125 1 0.30895795
## 4 poo.trend 4.929315 1 0.02640478
## ------
## --- GENE: MAFB ---
## ------- GxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 1.2360993 2 0.5389946
## 2 child 1.1715826 2 0.5566652
## 3 haplo.freq.trend 0.9720702 1 0.3241644
## 4 child.trend 0.5652687 1 0.4521452
## ------- PoOxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 2.797472 2 0.24690885
## 2 poo 2.304450 2 0.31593297
## 3 haplo.freq.trend 2.789360 1 0.09489213
## 4 poo.trend 1.949009 1 0.16269371
## ------
## 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: 11, 23, 27, 47, 56, 70 ... 666, 668, 669, 674, 676, 678
## INFO: Will select 103 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 103 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20804d4c7bb2.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/RtmpeWvLZW/ff20803ea531f9.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff208055e58d.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff20805f806511.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20802e36a5f.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff20801e0f6aef.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20807abd165d.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff208054033d7.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff208070b11af5.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff2080292230b2.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20804ef1195.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff208017c6318c.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff2080721130.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
## 35 34 34
##
## 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
gxe
test:## --- GENE: PAX7 ---
## ------- GxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 4.10293399 2 0.1285462
## 2 child 2.12642369 2 0.3453448
## 3 haplo.freq.trend 0.04333122 1 0.8351029
## 4 child.trend 0.42056658 1 0.5166545
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 2.88986112 2 0.2357624
## 2 poo 1.22148962 2 0.5429463
## 3 haplo.freq.trend 0.00417373 1 0.9484890
## 4 poo.trend 1.04762736 1 0.3060542
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 0.10755890 2 0.9476411
## 2 child 0.19512791 2 0.9070443
## 3 haplo.freq.trend 0.08960272 1 0.7646828
## 4 child.trend 0.18814426 1 0.6644656
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 0.10496666 2 0.9488701
## 2 poo 0.09576610 2 0.9532453
## 3 haplo.freq.trend 0.06500303 1 0.7987564
## 4 poo.trend 0.02947344 1 0.8636904
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 3.749656 2 0.1533813
## 2 child 4.569787 2 0.1017849
## 3 haplo.freq.trend 1.182969 1 0.2767523
## 4 child.trend 2.121689 1 0.1452263
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 2.02379770 2 0.36352804
## 2 poo 4.37686500 2 0.11209232
## 3 haplo.freq.trend 0.03806035 1 0.84532201
## 4 poo.trend 2.96353936 1 0.08516134
## ------
## --- GENE: 8q24 ---
## ------- GxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 1.9780213 2 0.3719445
## 2 child 1.7626185 2 0.4142402
## 3 haplo.freq.trend 1.0557697 1 0.3041820
## 4 child.trend 0.6047668 1 0.4367650
## ------- PoOxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 2.7185526 2 0.2568466
## 2 poo 1.2715494 2 0.5295251
## 3 haplo.freq.trend 1.3080040 1 0.2527564
## 4 poo.trend 0.1879751 1 0.6646073
## ------
## --- GENE: KIAA1598 ---
## ------- GxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 1.4457937 2 0.4853443
## 2 child 0.8411414 2 0.6566720
## 3 haplo.freq.trend 0.9542860 1 0.3286307
## 4 child.trend 0.5951628 1 0.4404296
## ------- PoOxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 1.7351383 2 0.4199712
## 2 poo 1.1886461 2 0.5519361
## 3 haplo.freq.trend 0.7048323 1 0.4011647
## 4 poo.trend 0.2799658 1 0.5967236
## ------
## --- GENE: SPRY2 ---
## ------- GxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 1.3173982 2 0.5175242
## 2 child 0.9216468 2 0.6307641
## 3 haplo.freq.trend 0.3480497 1 0.5552192
## 4 child.trend 0.8102143 1 0.3680569
## ------- PoOxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 0.8610075 2 0.65018148
## 2 poo 7.0490220 2 0.02946621
## 3 haplo.freq.trend 0.5800484 1 0.44629334
## 4 poo.trend 0.3925655 1 0.53095391
## ------
## 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: 11, 23, 27, 47, 56, 70 ... 666, 668, 669, 674, 676, 678
## INFO: Will select 103 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 103 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff208032da48bf.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/RtmpeWvLZW/ff2080190c7c72.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20805d6b15a3.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff20807eb3346f.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff2080af66320.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff20802e644c9.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff2080f047f1e.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
## 35 34 34
##
## 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: THADA ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 4
## INFO: Will select 103 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/RtmpeWvLZW/ff208078b26a6.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff2080ea510c2.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff2080595c7670.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20805900bd3.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff20801cdb1655.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20806bd02f3f.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
## 35 34 34
##
## 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 103 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/RtmpeWvLZW/ff2080625a60c5.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff208047e21396.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
## 35 34 34
##
## 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: MAFB ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 12
## INFO: Will select 103 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/RtmpeWvLZW/ff208068b74af8.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
## 35 34 34
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpeWvLZW/ff20801599498d.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
## 35 34 34
##
## 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 0.82220863 2 0.6629178
## 2 child 0.17185595 2 0.9176603
## 3 haplo.freq.trend 0.80645988 1 0.3691690
## 4 child.trend 0.03530719 1 0.8509534
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 0.8563413 2 0.6517002
## 2 poo 2.4453376 2 0.2944433
## 3 haplo.freq.trend 0.4499531 1 0.5023572
## 4 poo.trend 0.0482705 1 0.8261005
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 1.645555339 2 0.4392100
## 2 child 2.155842666 2 0.3403022
## 3 haplo.freq.trend 0.005877185 1 0.9388918
## 4 child.trend 1.692192598 1 0.1933122
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 7.918634365 2 0.01907614
## 2 poo 8.608869144 2 0.01350852
## 3 haplo.freq.trend 0.014448530 1 0.90432310
## 4 poo.trend 0.001109979 1 0.97342232
## ------
## --- GENE: IRF6 ---
## ------- GxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 1.61943169 2 0.4449845
## 2 child 3.67553669 2 0.1591722
## 3 haplo.freq.trend 0.07821491 1 0.7797312
## 4 child.trend 0.00288554 1 0.9571605
## ------- PoOxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 1.5104212 2 0.4699116
## 2 poo 0.1829955 2 0.9125634
## 3 haplo.freq.trend 0.2943362 1 0.5874551
## 4 poo.trend 0.1056566 1 0.7451443
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.162208509 2 0.9220976
## 2 child 0.073448616 2 0.9639418
## 3 haplo.freq.trend 0.007133777 1 0.9326894
## 4 child.trend 0.001094675 1 0.9736061
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.2930601 2 0.8636998
## 2 poo 2.1646735 2 0.3388029
## 3 haplo.freq.trend 0.2599119 1 0.6101807
## 4 poo.trend 1.7806075 1 0.1820747
## ------
## --- GENE: FOXE1 ---
## ------- GxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.9263609 2 0.6292791
## 2 child 0.4521087 2 0.7976747
## 3 haplo.freq.trend 0.6671608 1 0.4140432
## 4 child.trend 0.2401863 1 0.6240716
## ------- PoOxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.266292214 2 0.8753372
## 2 poo 1.118554144 2 0.5716222
## 3 haplo.freq.trend 0.253273721 1 0.6147793
## 4 poo.trend 0.002627365 1 0.9591201
## ------
## --- GENE: KIAA1598 ---
## ------- GxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 1.4457937 2 0.4853443
## 2 child 0.8411414 2 0.6566720
## 3 haplo.freq.trend 0.9542860 1 0.3286307
## 4 child.trend 0.5951628 1 0.4404296
## ------- PoOxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 1.7351383 2 0.4199712
## 2 poo 1.1886461 2 0.5519361
## 3 haplo.freq.trend 0.7048323 1 0.4011647
## 4 poo.trend 0.2799658 1 0.5967236
## ------
## --- GENE: TPM1 ---
## ------- GxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 0.07211337 2 0.9645856
## 2 child 0.91465359 2 0.6329735
## 3 haplo.freq.trend 0.01543425 1 0.9011295
## 4 child.trend 0.91464648 1 0.3388846
## ------- PoOxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 0.6179084 2 0.73421440
## 2 poo 5.1815009 2 0.07496376
## 3 haplo.freq.trend 0.5451233 1 0.46031717
## 4 poo.trend 1.6245113 1 0.20246389
## ------
## --- GENE: MAFB ---
## ------- GxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 0.48697920 2 0.7838876
## 2 child 0.16240890 2 0.9220052
## 3 haplo.freq.trend 0.09176895 1 0.7619402
## 4 child.trend 0.01502814 1 0.9024323
## ------- PoOxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 0.1979366 2 0.9057714
## 2 poo 1.7833353 2 0.4099715
## 3 haplo.freq.trend 0.1979277 1 0.6563988
## 4 poo.trend 0.6210006 1 0.4306757
## ------
## Saved image to file: GxM_PoOxM_new_betas_mult_ CLO .RData