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 CLP!
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,] 166 166 166 166 166 166 166 166 166 166 166
## [2,] 19 1 14 1 1 1 6 1 30 2 21
## PAX7 ABCA4 THADA 8q24 KIAA1598 SPRY2
## [1,] 166 166 166 166 166 166
## [2,] 1 6 1 1 1 1
## PAX7 ABCA4 IRF6 THADA FOXE1 KIAA1598 TPM1 MAFB
## [1,] 166 166 166 166 166 166 166 166
## [2,] 54 16 27 14 7 1 29 9
## Grouping limits, promoter regions:
## PAX7 ABCA4 IRF6 THADA 8q21.3
## 0% -0.96691483 -0.1244538 -0.9040936 -0.06567031 -0.04889268
## 33.33333% 0.04258831 0.9359239 0.1208876 0.95868248 0.97115570
## 66.66667% 0.04723040 0.9494929 0.1372878 0.96535248 0.97441041
## 100% 1.06086396 1.9705125 1.1947128 1.97611719 1.98632121
## 8q24 FOXE1 SPRY2 TPM1 NOG1
## 0% -0.6060226 -0.98794349 -0.04859895 -0.7814193 -0.5120293
## 33.33333% 0.7508203 0.01542281 0.97459638 0.2376595 0.5118647
## 66.66667% 0.8244217 0.01756489 0.97844535 0.2465935 0.5221919
## 100% 1.9248418 1.03090134 1.98594815 1.2709067 1.5579287
## MAFB
## 0% -0.94198720
## 33.33333% 0.07215136
## 66.66667% 0.07924527
## 100% 1.09590999
## Grouping limits, enhancer regions:
## PAX7 ABCA4 THADA 8q24 KIAA1598
## 0% -0.97289033 -0.06776287 -0.03621757 -0.05056983 -0.05018514
## 33.33333% 0.05056198 0.94623069 0.97658700 0.96851492 0.97082043
## 66.66667% 0.06311021 0.95026225 0.97945350 0.97285628 0.97487551
## 100% 1.10194979 1.95850337 1.98461539 1.98034143 1.98267764
## SPRY2
## 0% -0.2352023
## 33.33333% 0.8727414
## 66.66667% 0.8990984
## 100% 1.9566071
## Grouping limits, gene regions:
## PAX7 ABCA4 IRF6 THADA FOXE1
## 0% -0.8911824 -0.2447756 -0.5730036 -0.1540526 -0.94472579
## 33.33333% 0.1217193 0.8016359 0.4405855 0.8894449 0.07450210
## 66.66667% 0.1279638 0.8100850 0.4440570 0.9058691 0.08358899
## 100% 1.1436416 1.8333790 1.4520446 1.9464645 1.10222436
## KIAA1598 TPM1 MAFB
## 0% -0.05018514 -0.5312118 -0.96281233
## 33.33333% 0.97082043 0.4867602 0.05040960
## 66.66667% 0.97487551 0.4929923 0.05573132
## 100% 1.98267764 1.5007956 1.07272602
## 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: 1, 5, 8, 13, 15, 19 ... 671, 672, 675, 682, 683, 684
## INFO: Will select 166 rows and 72 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmpq6iF6H/ff4c44ce71911.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 166 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b78560771ab.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/RtmpAzMhD1/ff1b7840616082.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
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7811a02db1.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: ABCA4 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b785f663a64.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b78208d108a.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: IRF6 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 3
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_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/RtmpAzMhD1/ff1b782835409.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b783c80525c.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: THADA ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 4
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b784d202381.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
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7855c3333a.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: 8q21.3 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 5
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b783de050e.ff
## ...done, all alleles: A C
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b78e637d4a.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: 8q24 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 6
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b781e0e73a7.ff
## ...done, all alleles: A C
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b782cb3946.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: FOXE1 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 7
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b784ba84178.ff
## ...done, all alleles: C T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b781dc712fd.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: SPRY2 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 9
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7875924060.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b787f95dd1.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: TPM1 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 10
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b784213a72.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b786d682937.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: NOG1 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 11
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_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/RtmpAzMhD1/ff1b785541a75.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
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b785e74753a.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: MAFB ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 12
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b787e43465.ff
## ...done, all alleles: C T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData , ./data_subset3_promoter_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b783c4316f8.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
gxe
test:## --- GENE: PAX7 ---
## ------- GxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 2.861759 2 0.23909854
## 2 child 2.541217 2 0.28066084
## 3 haplo.freq.trend 2.819944 1 0.09309966
## 4 child.trend 1.858737 1 0.17277060
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 3.68773258 2 0.1582046
## 2 poo 3.57119280 2 0.1676970
## 3 haplo.freq.trend 2.39018853 1 0.1220989
## 4 poo.trend 0.01186043 1 0.9132774
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 1.2282543 2 0.5411130
## 2 child 2.7623479 2 0.2512834
## 3 haplo.freq.trend 0.6742613 1 0.4115699
## 4 child.trend 1.9716667 1 0.1602711
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 1.37658412 2 0.5024335
## 2 poo 0.02757870 2 0.9863053
## 3 haplo.freq.trend 0.64372584 1 0.4223648
## 4 poo.trend 0.02537926 1 0.8734257
## ------
## --- GENE: IRF6 ---
## ------- GxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 0.9675554 2 0.6164502
## 2 child 0.4269444 2 0.8077746
## 3 haplo.freq.trend 0.4961615 1 0.4811916
## 4 child.trend 0.1585753 1 0.6904716
## ------- PoOxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 5.04365258 2 0.08031280
## 2 poo 6.02085249 2 0.04927067
## 3 haplo.freq.trend 0.01102776 1 0.91636540
## 4 poo.trend 1.54088474 1 0.21448616
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.8170012 2 0.6646461
## 2 child 0.9373886 2 0.6258189
## 3 haplo.freq.trend 0.8057217 1 0.3693882
## 4 child.trend 0.7934143 1 0.3730697
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.3446746 2 0.8416952
## 2 poo 0.5335331 2 0.7658518
## 3 haplo.freq.trend 0.3018063 1 0.5827522
## 4 poo.trend 0.3379354 1 0.5610234
## ------
## --- GENE: 8q21.3 ---
## ------- GxM: 8q21.3
## gxe.test chisq df pval
## 1 haplo.freq 2.9119837 2 0.2331690
## 2 child 2.4832782 2 0.2889103
## 3 haplo.freq.trend 1.0209285 1 0.3122989
## 4 child.trend 0.1559651 1 0.6928988
## ------- PoOxM: 8q21.3
## gxe.test chisq df pval
## 1 haplo.freq 5.5296311 2 0.06298772
## 2 poo 1.1243141 2 0.56997828
## 3 haplo.freq.trend 1.9861543 1 0.15874356
## 4 poo.trend 0.3086436 1 0.57851372
## ------
## --- GENE: 8q24 ---
## ------- GxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 0.5331141 2 0.76601229
## 2 child 3.1211853 2 0.21001157
## 3 haplo.freq.trend 0.1456132 1 0.70276326
## 4 child.trend 2.8003930 1 0.09424121
## ------- PoOxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 8.24397387 2 0.016212270
## 2 poo 11.22412734 2 0.003653522
## 3 haplo.freq.trend 0.09570691 1 0.757043637
## 4 poo.trend 2.91985280 1 0.087495845
## ------
## --- GENE: FOXE1 ---
## ------- GxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.06881897 2 0.9661758
## 2 child 0.70284135 2 0.7036877
## 3 haplo.freq.trend 0.06189607 1 0.8035238
## 4 child.trend 0.55397220 1 0.4566992
## ------- PoOxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 1.0020007 2 0.6059242
## 2 poo 2.5850672 2 0.2745742
## 3 haplo.freq.trend 0.7657994 1 0.3815197
## 4 poo.trend 1.6207861 1 0.2029822
## ------
## --- GENE: SPRY2 ---
## ------- GxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 0.8740345 2 0.64596030
## 2 child 3.0549616 2 0.21708185
## 3 haplo.freq.trend 0.7619605 1 0.38271568
## 4 child.trend 3.0427904 1 0.08109641
## ------- PoOxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 1.1183523 2 0.5716798
## 2 poo 0.2501057 2 0.8824503
## 3 haplo.freq.trend 0.8735155 1 0.3499839
## 4 poo.trend 0.0942142 1 0.7588865
## ------
## --- GENE: TPM1 ---
## ------- GxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 3.45184742 2 0.1780085
## 2 child 2.93682972 2 0.2302902
## 3 haplo.freq.trend 2.12208069 1 0.1451892
## 4 child.trend 0.06423886 1 0.7999175
## ------- PoOxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 4.9344824 2 0.08481853
## 2 poo 2.2243113 2 0.32884931
## 3 haplo.freq.trend 2.0963084 1 0.14765526
## 4 poo.trend 0.4339353 1 0.51006426
## ------
## --- GENE: NOG1 ---
## ------- GxM: NOG1
## gxe.test chisq df pval
## 1 haplo.freq 0.035287043 2 0.9825112
## 2 child 0.480635198 2 0.7863781
## 3 haplo.freq.trend 0.000349412 1 0.9850864
## 4 child.trend 0.328594237 1 0.5664880
## ------- PoOxM: NOG1
## gxe.test chisq df pval
## 1 haplo.freq 3.575391 2 0.167345369
## 2 poo 9.359562 2 0.009281047
## 3 haplo.freq.trend 2.058637 1 0.151345539
## 4 poo.trend 4.879195 1 0.027182298
## ------
## --- GENE: MAFB ---
## ------- GxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 0.15945594 2 0.9233675
## 2 child 0.09028866 2 0.9558595
## 3 haplo.freq.trend 0.09602006 1 0.7566590
## 4 child.trend 0.06371702 1 0.8007147
## ------- PoOxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 2.7214436 2 0.2564756
## 2 poo 4.3441945 2 0.1139384
## 3 haplo.freq.trend 0.5955426 1 0.4402838
## 4 poo.trend 0.1976256 1 0.6566442
## ------
## 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: 1, 5, 8, 13, 15, 19 ... 671, 672, 675, 682, 683, 684
## INFO: Will select 166 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 166 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b78b3f1d23.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/RtmpAzMhD1/ff1b7814af2544.ff
## ...done, all alleles: G T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b785f5053e1.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
## === GENE: ABCA4 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b783a45d56.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b781071afa.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: THADA ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 4
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b785c3f4d2d.ff
## ...done, all alleles: G T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b78f8d4bf2.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: 8q24 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 6
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_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/RtmpAzMhD1/ff1b783a9467a1.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
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b783fca473a.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "3"...Done
## === GENE: KIAA1598 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 8
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_enhancer_GxM_gen.ffData, ./data_subset2_enhancer_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b787c1295f.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b787e3349fa.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: SPRY2 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 9
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_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/RtmpAzMhD1/ff1b785344567.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_enhancer_GxM_gen.ffData , ./data_subset3_enhancer_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b786837268e.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
gxe
test:## --- GENE: PAX7 ---
## ------- GxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 2.2117623 2 0.3309192
## 2 child 1.3834261 2 0.5007176
## 3 haplo.freq.trend 1.1009601 1 0.2940555
## 4 child.trend 0.7281482 1 0.3934841
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 0.06662149 2 0.96723795
## 2 poo 5.56260845 2 0.06195765
## 3 haplo.freq.trend 0.01348262 1 0.90756164
## 4 poo.trend 1.70124962 1 0.19212464
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 4.5732307 2 0.1016098
## 2 child 1.6846591 2 0.4307060
## 3 haplo.freq.trend 0.3115964 1 0.5767022
## 4 child.trend 0.2029797 1 0.6523264
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 5.55427960 2 0.0622162
## 2 poo 1.12781043 2 0.5689827
## 3 haplo.freq.trend 0.06335070 1 0.8012763
## 4 poo.trend 0.01041093 1 0.9187297
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.13630940 2 0.9341160
## 2 child 0.21276007 2 0.8990829
## 3 haplo.freq.trend 0.06012291 1 0.8063018
## 4 child.trend 0.11111201 1 0.7388817
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 2.055122 2 0.35787869
## 2 poo 3.849899 2 0.14588313
## 3 haplo.freq.trend 1.902384 1 0.16781174
## 4 poo.trend 3.481832 1 0.06204603
## ------
## --- GENE: 8q24 ---
## ------- GxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 1.6282301 2 0.4430312
## 2 child 1.2250035 2 0.5419933
## 3 haplo.freq.trend 0.6430168 1 0.4226205
## 4 child.trend 0.2744515 1 0.6003612
## ------- PoOxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 1.15750051 2 0.5605985
## 2 poo 0.17192327 2 0.9176294
## 3 haplo.freq.trend 0.65000406 1 0.4201112
## 4 poo.trend 0.01794171 1 0.8934447
## ------
## --- GENE: KIAA1598 ---
## ------- GxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.5042030 2 0.7771658
## 2 child 1.6445884 2 0.4394224
## 3 haplo.freq.trend 0.4216944 1 0.5160928
## 4 child.trend 0.5851293 1 0.4443088
## ------- PoOxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 2.106208 2 0.34885314
## 2 poo 5.067318 2 0.07936808
## 3 haplo.freq.trend 1.756028 1 0.18512075
## 4 poo.trend 4.733945 1 0.02957298
## ------
## --- GENE: SPRY2 ---
## ------- GxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 8.533000 2 0.01403080
## 2 child 2.790173 2 0.24781166
## 3 haplo.freq.trend 2.941893 1 0.08630952
## 4 child.trend 2.408040 1 0.12071343
## ------- PoOxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 4.1671347 2 0.1244853
## 2 poo 8.3161026 2 0.0156380
## 3 haplo.freq.trend 0.8403891 1 0.3592855
## 4 poo.trend 1.2299492 1 0.2674169
## ------
## 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: 1, 5, 8, 13, 15, 19 ... 671, 672, 675, 682, 683, 684
## INFO: Will select 166 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 166 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7832276d04.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/RtmpAzMhD1/ff1b782ced5be9.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
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b783711657b.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: ABCA4 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_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/RtmpAzMhD1/ff1b781cffefd.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7828c28f9.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: IRF6 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 3
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b783b1369ad.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b782dfb65db.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: THADA ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 4
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7818ba4f9e.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
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b787e922c5a.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...
## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: FOXE1 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 7
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_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/RtmpAzMhD1/ff1b785fa9c67.ff
## ...done, all alleles: C T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7870e37281.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: KIAA1598 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 8
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_gene_GxM_gen.ffData, ./data_subset2_gene_GxM_gen.RData
## 2. adding strata information and preprocessing data:
## The output file(s) exist!
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
## ...running on only one CPU core! This may take some time...
## ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b78394417.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b78644f10b1.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: TPM1 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 10
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_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/RtmpAzMhD1/ff1b786fe633af.ff
## ...done, all alleles: A G
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b783bb74e1e.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
## === GENE: MAFB ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 12
## INFO: Will select 166 rows and 6 columns.
## Saving data...
## ... saved to files: ./data_subset2_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/RtmpAzMhD1/ff1b7877d041a4.ff
## ...done, all alleles: C T
## ...recoding SNPs...
## ...done
## Saving data...
## ... saved to files: ./data_subset3_gene_GxM_gen.ffData , ./data_subset3_gene_GxM_gen.RData
## 3. running haplinStrat:
## 3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7868055d50.ff
## Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
##
## 3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
##
## ## Running haplinStrat ##
##
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
## 1 2 3
## 56 55 55
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
gxe
test:## --- GENE: PAX7 ---
## ------- GxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 3.735337 2 0.1544834
## 2 child 3.311433 2 0.1909552
## 3 haplo.freq.trend 2.293229 1 0.1299394
## 4 child.trend 2.744882 1 0.0975663
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 2.2962884 2 0.3172249
## 2 poo 0.8134483 2 0.6658278
## 3 haplo.freq.trend 2.1649695 1 0.1411874
## 4 poo.trend 0.1110324 1 0.7389718
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 1.7064012 2 0.4260491
## 2 child 0.7513144 2 0.6868377
## 3 haplo.freq.trend 1.2335796 1 0.2667120
## 4 child.trend 0.7128921 1 0.3984854
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 0.61241469 2 0.7362339
## 2 poo 1.97540610 2 0.3724312
## 3 haplo.freq.trend 0.61046710 1 0.4346120
## 4 poo.trend 0.04919088 1 0.8244772
## ------
## --- GENE: IRF6 ---
## ------- GxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 0.5768089 2 0.7494584
## 2 child 0.2424825 2 0.8858202
## 3 haplo.freq.trend 0.3513508 1 0.5533495
## 4 child.trend 0.2005136 1 0.6543066
## ------- PoOxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 5.1264441 2 0.07705606
## 2 poo 8.4213005 2 0.01483672
## 3 haplo.freq.trend 0.2081734 1 0.64820289
## 4 poo.trend 0.1198653 1 0.72918063
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.34425642 2 0.8418712
## 2 child 0.05048282 2 0.9750745
## 3 haplo.freq.trend 0.24847219 1 0.6181529
## 4 child.trend 0.03904531 1 0.8433589
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.641903322 2 0.7254583
## 2 poo 0.764141817 2 0.6824467
## 3 haplo.freq.trend 0.252666848 1 0.6152035
## 4 poo.trend 0.004575061 1 0.9460728
## ------
## --- GENE: FOXE1 ---
## ------- GxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 5.118318 2 0.0773697632
## 2 child 13.737521 2 0.0010397648
## 3 haplo.freq.trend 3.495759 1 0.0615261881
## 4 child.trend 13.178428 1 0.0002831902
## ------- PoOxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 6.43401878 2 0.04007473
## 2 poo 3.37817245 2 0.18468821
## 3 haplo.freq.trend 1.60857927 1 0.20469163
## 4 poo.trend 0.07046808 1 0.79065648
## ------
## --- GENE: KIAA1598 ---
## ------- GxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.5042030 2 0.7771658
## 2 child 1.6445884 2 0.4394224
## 3 haplo.freq.trend 0.4216944 1 0.5160928
## 4 child.trend 0.5851293 1 0.4443088
## ------- PoOxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 2.106208 2 0.34885314
## 2 poo 5.067318 2 0.07936808
## 3 haplo.freq.trend 1.756028 1 0.18512075
## 4 poo.trend 4.733945 1 0.02957298
## ------
## --- GENE: TPM1 ---
## ------- GxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 1.1479872 2 0.5632714
## 2 child 1.9083615 2 0.3851275
## 3 haplo.freq.trend 1.0846332 1 0.2976634
## 4 child.trend 0.9943185 1 0.3186892
## ------- PoOxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 2.850261 2 0.2404771
## 2 poo 3.079383 2 0.2144472
## 3 haplo.freq.trend 2.339848 1 0.1261018
## 4 poo.trend 1.193394 1 0.2746460
## ------
## --- GENE: MAFB ---
## ------- GxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 1.0349270 2 0.5960305
## 2 child 0.3433655 2 0.8422463
## 3 haplo.freq.trend 0.6891146 1 0.4064657
## 4 child.trend 0.3282741 1 0.5666771
## ------- PoOxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 1.55076888 2 0.4605267
## 2 poo 3.87174409 2 0.1442984
## 3 haplo.freq.trend 0.01039569 1 0.9187890
## 4 poo.trend 0.84561780 1 0.3577950
## ------
## Saved image to file: GxM_PoOxM_new_betas_mult_ CLP .RData