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 CL/P!
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,] 269 269 269 269 269 269 269 269 269 269 269
## [2,] 19 1 14 1 1 1 6 1 30 2 21
## PAX7 ABCA4 THADA 8q24 KIAA1598 SPRY2
## [1,] 269 269 269 269 269 269
## [2,] 1 6 1 1 1 1
## PAX7 ABCA4 IRF6 THADA FOXE1 KIAA1598 TPM1 MAFB
## [1,] 269 269 269 269 269 269 269 269
## [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 -0.07298237 -0.04989332
## 33.33333% 0.04172604 0.9339726 0.1212811 0.95824528 0.97145945
## 66.66667% 0.04696595 0.9471321 0.1379738 0.96544083 0.97515808
## 100% 1.06086396 1.9705125 1.1947128 1.97900957 1.98632121
## 8q24 FOXE1 SPRY2 TPM1 NOG1
## 0% -0.6060226 -0.98812215 -0.04906648 -0.7922317 -0.5120293
## 33.33333% 0.7595575 0.01519656 0.97349709 0.2365493 0.5118704
## 66.66667% 0.8255510 0.01760980 0.97799848 0.2457710 0.5216657
## 100% 1.9248418 1.03090134 1.98594815 1.2709067 1.5606337
## MAFB
## 0% -0.94418914
## 33.33333% 0.07211143
## 66.66667% 0.07915924
## 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% 0.05026514 0.94599639 0.97642517 0.96801790 0.97083932
## 66.66667% 0.06255916 0.95038313 0.97927125 0.97225732 0.97511456
## 100% 1.10194979 1.96131206 1.98866802 1.98308790 1.98267764
## SPRY2
## 0% -0.2352023
## 33.33333% 0.8673211
## 66.66667% 0.8967899
## 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% 0.1214664 0.8012154 0.4403448 0.8908858 0.07453864
## 66.66667% 0.1278515 0.8094471 0.4439450 0.9064252 0.08386644
## 100% 1.1438084 1.8333790 1.4536303 1.9464645 1.10222436
## KIAA1598 TPM1 MAFB
## 0% -0.05330819 -0.5319530 -0.96281233
## 33.33333% 0.97083932 0.4863991 0.04921442
## 66.66667% 0.97511456 0.4926761 0.05539040
## 100% 1.98267764 1.5007956 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: 1, 5, 8, 11, 13, 15 ... 675, 676, 678, 682, 683, 684
## INFO: Will select 269 rows and 72 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmpq6iF6H/ff4c4180052a6.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 269 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b85ba34089.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/RtmpKONFQN/ff14b83ed2379.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b836f77c40.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b81d676727.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b88b9349b.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b84eaa73c3.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b876cc8a2.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b87dc01069.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b82a5341e.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b839121dcd.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b85919494d.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b854cf2ab4.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b8440a115e.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b85d697877.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b845b57cf7.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b81a144f87.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b870d134b2.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b81f4a23e4.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b83eb5599c.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b871499a4.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b84dde45b5.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b836937973.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b8306c1c72.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
## 90 89 90
##
## 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 0.8896285 2 0.6409433
## 2 child 3.2491755 2 0.1969929
## 3 haplo.freq.trend 0.7193426 1 0.3963596
## 4 child.trend 0.5350023 1 0.4645114
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 0.7466988 2 0.6884247
## 2 poo 1.4254403 2 0.4903087
## 3 haplo.freq.trend 0.1129623 1 0.7367965
## 4 poo.trend 0.3976523 1 0.5283042
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 0.4843100 2 0.7849345
## 2 child 0.4951355 2 0.7806973
## 3 haplo.freq.trend 0.1394102 1 0.7088681
## 4 child.trend 0.2935725 1 0.5879402
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 0.3559978 2 0.8369433
## 2 poo 0.5359988 2 0.7649082
## 3 haplo.freq.trend 0.3250819 1 0.5685695
## 4 poo.trend 0.2388530 1 0.6250358
## ------
## --- GENE: IRF6 ---
## ------- GxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 0.34967685 2 0.8395927
## 2 child 0.44956413 2 0.7986903
## 3 haplo.freq.trend 0.33925120 1 0.5602618
## 4 child.trend 0.05471564 1 0.8150519
## ------- PoOxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 0.2236279 2 0.8942106
## 2 poo 2.1750822 2 0.3370442
## 3 haplo.freq.trend 0.1005148 1 0.7512127
## 4 poo.trend 1.8888564 1 0.1693310
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.427764691 2 0.8074434
## 2 child 0.715079088 2 0.6993950
## 3 haplo.freq.trend 0.001371029 1 0.9704631
## 4 child.trend 0.304579003 1 0.5810259
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 0.6855080 2 0.7098128
## 2 poo 1.6578891 2 0.4365098
## 3 haplo.freq.trend 0.3439544 1 0.5575555
## 4 poo.trend 1.5640993 1 0.2110660
## ------
## --- GENE: 8q21.3 ---
## ------- GxM: 8q21.3
## gxe.test chisq df pval
## 1 haplo.freq 8.33897659 2 0.01546017
## 2 child 8.79430069 2 0.01231238
## 3 haplo.freq.trend 0.09474415 1 0.75823043
## 4 child.trend 0.14242375 1 0.70588327
## ------- PoOxM: 8q21.3
## gxe.test chisq df pval
## 1 haplo.freq 9.95115571 2 0.006904528
## 2 poo 1.73188160 2 0.420655613
## 3 haplo.freq.trend 0.05148402 1 0.820500797
## 4 poo.trend 0.05853343 1 0.808829119
## ------
## --- GENE: 8q24 ---
## ------- GxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 1.666438 2 0.43464800
## 2 child 4.276095 2 0.11788477
## 3 haplo.freq.trend 1.018611 1 0.31284863
## 4 child.trend 3.611729 1 0.05737344
## ------- PoOxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 2.8470872 2 0.2408590
## 2 poo 5.6799407 2 0.0584274
## 3 haplo.freq.trend 0.3494898 1 0.5544021
## 4 poo.trend 0.8818528 1 0.3476947
## ------
## --- GENE: FOXE1 ---
## ------- GxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 0.201342023 2 0.9042305
## 2 child 0.851989873 2 0.6531196
## 3 haplo.freq.trend 0.000158224 1 0.9899639
## 4 child.trend 0.259787738 1 0.6102660
## ------- PoOxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 1.223469 2 0.54240924
## 2 poo 5.658634 2 0.05905318
## 3 haplo.freq.trend 1.216005 1 0.27014615
## 4 poo.trend 5.161054 1 0.02309888
## ------
## --- GENE: SPRY2 ---
## ------- GxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 3.502844 2 0.17352698
## 2 child 5.724609 2 0.05713693
## 3 haplo.freq.trend 2.850083 1 0.09136924
## 4 child.trend 5.251933 1 0.02192240
## ------- PoOxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 4.9931692 2 0.08236583
## 2 poo 2.1348558 2 0.34389191
## 3 haplo.freq.trend 2.7792198 1 0.09549468
## 4 poo.trend 0.1702504 1 0.67988937
## ------
## --- GENE: TPM1 ---
## ------- GxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 2.8691629 2 0.2382151
## 2 child 2.4012031 2 0.3010131
## 3 haplo.freq.trend 2.6850346 1 0.1012950
## 4 child.trend 0.1105556 1 0.7395125
## ------- PoOxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 4.4676825 2 0.10711618
## 2 poo 4.1342405 2 0.12654969
## 3 haplo.freq.trend 2.9967377 1 0.08343236
## 4 poo.trend 0.5738001 1 0.44875281
## ------
## --- GENE: NOG1 ---
## ------- GxM: NOG1
## gxe.test chisq df pval
## 1 haplo.freq 0.19045913 2 0.9091642
## 2 child 0.49606300 2 0.7803354
## 3 haplo.freq.trend 0.01325687 1 0.9083354
## 4 child.trend 0.14694742 1 0.7014698
## ------- PoOxM: NOG1
## gxe.test chisq df pval
## 1 haplo.freq 3.4403495 2 0.179034855
## 2 poo 11.4745355 2 0.003223564
## 3 haplo.freq.trend 0.8769649 1 0.349034319
## 4 poo.trend 0.8427321 1 0.358616546
## ------
## --- GENE: MAFB ---
## ------- GxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 0.12156181 2 0.9410294
## 2 child 0.25827094 2 0.8788549
## 3 haplo.freq.trend 0.11981516 1 0.7292350
## 4 child.trend 0.05776931 1 0.8100570
## ------- PoOxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 1.6433540 2 0.4396937
## 2 poo 4.4983069 2 0.1054885
## 3 haplo.freq.trend 0.5318892 1 0.4658137
## 4 poo.trend 0.6301914 1 0.4272851
## ------
## 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, 11, 13, 15 ... 675, 676, 678, 682, 683, 684
## INFO: Will select 269 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 269 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b84aa52b3e.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/RtmpKONFQN/ff14b83e6572d7.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b842a560d4.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b855d2485b.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b87b5b6804.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b82c0b1f7.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b861364ece.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b8bf43d8a.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b856904494.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b837d46127.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b8198574cd.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b81fd43395.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b876784b83.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
## 90 89 90
##
## 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 3.1852470 2 0.2033913
## 2 child 1.0420931 2 0.5938987
## 3 haplo.freq.trend 0.8198434 1 0.3652260
## 4 child.trend 0.4254631 1 0.5142236
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 0.78041524 2 0.6769163
## 2 poo 1.66559076 2 0.4348321
## 3 haplo.freq.trend 0.37155503 1 0.5421579
## 4 poo.trend 0.04496136 1 0.8320751
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 1.9749894 2 0.3725088
## 2 child 0.8733815 2 0.6461712
## 3 haplo.freq.trend 0.3663283 1 0.5450125
## 4 child.trend 0.2539041 1 0.6143394
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 2.92747713 2 0.2313697
## 2 poo 1.20299566 2 0.5479902
## 3 haplo.freq.trend 0.06054027 1 0.8056440
## 4 poo.trend 0.02868316 1 0.8655127
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 3.1259252 2 0.2095144
## 2 child 1.4432644 2 0.4859584
## 3 haplo.freq.trend 0.6673573 1 0.4139745
## 4 child.trend 0.7807533 1 0.3769108
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 3.1668742 2 0.20526836
## 2 poo 5.8239839 2 0.05436733
## 3 haplo.freq.trend 0.4234795 1 0.51520591
## 4 poo.trend 5.6222047 1 0.01773433
## ------
## --- GENE: 8q24 ---
## ------- GxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 1.861817 2 0.3941955
## 2 child 1.598284 2 0.4497147
## 3 haplo.freq.trend 1.212689 1 0.2708003
## 4 child.trend 0.744796 1 0.3881289
## ------- PoOxM: 8q24
## gxe.test chisq df pval
## 1 haplo.freq 1.42967406 2 0.4892718
## 2 poo 0.28393215 2 0.8676507
## 3 haplo.freq.trend 1.14817482 1 0.2839316
## 4 poo.trend 0.06956909 1 0.7919652
## ------
## --- GENE: KIAA1598 ---
## ------- GxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.2167960 2 0.8972704
## 2 child 0.9128842 2 0.6335337
## 3 haplo.freq.trend 0.1644054 1 0.6851325
## 4 child.trend 0.4975054 1 0.4805983
## ------- PoOxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 1.0967114 2 0.57789928
## 2 poo 4.0124674 2 0.13449427
## 3 haplo.freq.trend 0.9519186 1 0.32923140
## 4 poo.trend 3.8015809 1 0.05120422
## ------
## --- GENE: SPRY2 ---
## ------- GxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 3.739347 2 0.15417397
## 2 child 3.892916 2 0.14277888
## 3 haplo.freq.trend 2.799699 1 0.09428202
## 4 child.trend 3.876910 1 0.04895458
## ------- PoOxM: SPRY2
## gxe.test chisq df pval
## 1 haplo.freq 2.52488622 2 0.2829619
## 2 poo 0.99322375 2 0.6085891
## 3 haplo.freq.trend 2.35584055 1 0.1248146
## 4 poo.trend 0.04297031 1 0.8357812
## ------
## 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, 11, 13, 15 ... 675, 676, 678, 682, 683, 684
## INFO: Will select 269 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 269 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b8a8f9d4.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/RtmpKONFQN/ff14b83ce040a1.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b85ff371d7.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b86edd64d5.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b82f1c2b3d.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b875aa1b29.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b83ddc6721.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b8753b5523.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b847f71dc4.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b82987419b.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b84c944b97.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b8410b593c.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b844bc9c2.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b847453b07.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b869de76a1.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
## 90 89 90
##
## 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 269 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/RtmpKONFQN/ff14b81f3a58d0.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
## 90 89 90
##
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpKONFQN/ff14b8c4d6e42.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
## 90 89 90
##
## Running Haplin on full data file...Done
##
## Running Haplin on stratum "1"...Done
##
## Running Haplin on stratum "2"...Done
##
## Running Haplin on stratum "3"...Done
gxe
test:## --- GENE: PAX7 ---
## ------- GxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 1.1412109 2 0.5651831
## 2 child 2.4321168 2 0.2963961
## 3 haplo.freq.trend 0.5611387 1 0.4538018
## 4 child.trend 2.0349173 1 0.1537225
## ------- PoOxM: PAX7
## gxe.test chisq df pval
## 1 haplo.freq 0.633947523 2 0.7283499
## 2 poo 0.004588727 2 0.9977083
## 3 haplo.freq.trend 0.261806664 1 0.6088817
## 4 poo.trend 0.004245033 1 0.9480515
## ------
## --- GENE: ABCA4 ---
## ------- GxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 2.2901448 2 0.3182009
## 2 child 4.2127460 2 0.1216785
## 3 haplo.freq.trend 0.3633952 1 0.5466266
## 4 child.trend 3.4284660 1 0.0640816
## ------- PoOxM: ABCA4
## gxe.test chisq df pval
## 1 haplo.freq 1.228433841 2 0.5410644
## 2 poo 0.195707123 2 0.9067817
## 3 haplo.freq.trend 0.155176076 1 0.6936372
## 4 poo.trend 0.004239173 1 0.9480873
## ------
## --- GENE: IRF6 ---
## ------- GxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 0.2026910 2 0.9036208
## 2 child 1.0574435 2 0.5893578
## 3 haplo.freq.trend 0.2019187 1 0.6531766
## 4 child.trend 0.1635910 1 0.6858717
## ------- PoOxM: IRF6
## gxe.test chisq df pval
## 1 haplo.freq 4.53825749 2 0.10340223
## 2 poo 8.48911482 2 0.01434208
## 3 haplo.freq.trend 0.23778493 1 0.62581056
## 4 poo.trend 0.00815675 1 0.92803712
## ------
## --- GENE: THADA ---
## ------- GxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 2.689947309 2 0.2605466
## 2 child 0.885036916 2 0.6424165
## 3 haplo.freq.trend 0.435900235 1 0.5091079
## 4 child.trend 0.005870831 1 0.9389248
## ------- PoOxM: THADA
## gxe.test chisq df pval
## 1 haplo.freq 1.57486276 2 0.4550120
## 2 poo 1.43961019 2 0.4868471
## 3 haplo.freq.trend 0.01052084 1 0.9183033
## 4 poo.trend 1.42005051 1 0.2333951
## ------
## --- GENE: FOXE1 ---
## ------- GxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 1.0310655 2 0.59718235
## 2 child 5.3575501 2 0.06864719
## 3 haplo.freq.trend 0.7066592 1 0.40055512
## 4 child.trend 5.3575176 1 0.02063312
## ------- PoOxM: FOXE1
## gxe.test chisq df pval
## 1 haplo.freq 3.422954959 2 0.18059876
## 2 poo 6.424730128 2 0.04026128
## 3 haplo.freq.trend 0.514502824 1 0.47319609
## 4 poo.trend 0.006029396 1 0.93810712
## ------
## --- GENE: KIAA1598 ---
## ------- GxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 0.2167960 2 0.8972704
## 2 child 0.9128842 2 0.6335337
## 3 haplo.freq.trend 0.1644054 1 0.6851325
## 4 child.trend 0.4975054 1 0.4805983
## ------- PoOxM: KIAA1598
## gxe.test chisq df pval
## 1 haplo.freq 1.0967114 2 0.57789928
## 2 poo 4.0124674 2 0.13449427
## 3 haplo.freq.trend 0.9519186 1 0.32923140
## 4 poo.trend 3.8015809 1 0.05120422
## ------
## --- GENE: TPM1 ---
## ------- GxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 1.8610823 2 0.3943403
## 2 child 0.3529697 2 0.8382115
## 3 haplo.freq.trend 1.8177588 1 0.1775803
## 4 child.trend 0.1266893 1 0.7218897
## ------- PoOxM: TPM1
## gxe.test chisq df pval
## 1 haplo.freq 3.323150 2 0.18983978
## 2 poo 1.730403 2 0.42096677
## 3 haplo.freq.trend 3.323022 1 0.06831616
## 4 poo.trend 1.619888 1 0.20310743
## ------
## --- GENE: MAFB ---
## ------- GxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 1.9537545 2 0.3764849
## 2 child 0.4118230 2 0.8139051
## 3 haplo.freq.trend 0.6498751 1 0.4201574
## 4 child.trend 0.1377913 1 0.7104868
## ------- PoOxM: MAFB
## gxe.test chisq df pval
## 1 haplo.freq 4.05150623 2 0.1318945
## 2 poo 3.10782935 2 0.2114187
## 3 haplo.freq.trend 0.54722606 1 0.4594533
## 4 poo.trend 0.03108084 1 0.8600602
## ------
## Saved image to file: GxM_PoOxM_new_betas_mult_ CLorP .RData