GxM, betas, multiplicative model, using randomly chosen 20 SNPs
Julia Romanowska
2019-10-17
Introduction
I chose those SNPs (from Moreno et al., 2017):
## no Marker chr coordinate gene_name
## 1 1 rs633265 18 57831468 <NA>
## 2 2 rs4621895 9 20582556 ENSG00000171843
## 3 3 rs1546124 16 84872051 ENSG00000103196
## 4 4 rs3750817 10 123332577 ENSG00000066468
## 5 5 rs2981428 10 123329429 ENSG00000066468
## 6 6 rs10984103 9 100639275 <NA>
## 7 7 rs9939609 16 53820527 ENSG00000140718
## 8 8 rs6010718 20 62719376 ENSG00000125510
## 9 9 rs17782313 18 57851097 <NA>
## 10 10 rs3752462 22 36710183 ENSG00000100345
## 11 11 rs2867125 2 622827 <NA>
## 12 12 rs2912771 10 123299297 ENSG00000066468
## 13 13 rs6659735 1 18983697 ENSG00000009709
## 14 14 rs10767664 11 27725986 ENSG00000255496
## 15 15 rs7138803 12 50247468 <NA>
## 16 16 rs17760296 17 54615617 <NA>
## 17 17 rs713586 2 25158008 <NA>
## 18 18 rs1443433 9 100579219 <NA>
## 19 19 rs4752566 10 123267631 ENSG00000066468
## 20 20 rs10818094 9 100563828 <NA>NOTE: all the genome positions here are from build hg19!
These analyses are for cleft type CL/P!
Data preparations
The data was prepared as in the file: preparing_new_betas_POO_ensembl-db.R, in short:
- identification of promoter and enhancer regions around the chosen SNPs, based on the regulatory ensembl database (build 37),
- extracting the matching data from both datasets, genomic and methylation
This gives the following data dimensions:
- for the promoter region:
## rs4621895 rs1546124 rs3750817 rs2981428 rs10984103 rs9939609
## [1,] 269 269 269 269 269 269
## [2,] 7 2 5 5 6 1
## rs6010718 rs3752462 rs2867125 rs2912771 rs6659735 rs10767664
## [1,] 269 269 269 269 269 269
## [2,] 21 2 1 1 19 32
## rs7138803 rs713586 rs1443433 rs4752566
## [1,] 269 269 269 269
## [2,] 11 15 6 3- for the enhancer region:
## rs3750817 rs2981428 rs2912771 rs6659735 rs7138803 rs713586
## [1,] 269 269 269 269 269 269
## [2,] 1 1 1 1 1 1- for the gene region:
## rs4621895 rs1546124 rs3750817 rs2981428 rs9939609 rs6010718 rs3752462
## [1,] 269 269 269 269 269 269 269
## [2,] 6 27 36 36 6 23 28
## rs2912771 rs6659735 rs10767664 rs4752566
## [1,] 269 269 269 269
## [2,] 20 55 65 21Categorizing methylation values
- sum up and average the beta values from all CpGs within the region
- divide into three categories: low, medium and high values
Divide the individuals in three groups (created by calculating the 33% and 66% quantiles)
## Grouping limits, promoter regions:## rs4621895 rs1546124 rs3750817 rs2981428 rs10984103
## 0% -0.96989876 -0.1155154 -0.06340883 -0.06340883 -0.98812215
## 33.33333% 0.04829741 0.9240675 0.95686104 0.95686104 0.01519656
## 66.66667% 0.05989188 0.9312628 0.96134288 0.96134288 0.01760980
## 100% 1.10573687 1.9602185 1.97164376 1.97164376 1.03090134
## rs9939609 rs6010718 rs3752462 rs2867125 rs2912771
## 0% -0.0641064 -0.8827719 -0.995188216 -0.7454512 -0.06413668
## 33.33333% 0.9651577 0.1316556 0.008651065 0.5781050 0.96339591
## 66.66667% 0.9723316 0.1370789 0.010649133 0.6527596 0.96911754
## 100% 1.9872540 1.1542372 1.015542014 1.8485176 1.98203170
## rs6659735 rs10767664 rs7138803 rs713586 rs1443433
## 0% -0.96691483 -0.98064055 -0.8165314 -0.6355066 -0.98812215
## 33.33333% 0.04172604 0.02671153 0.1875003 0.4056576 0.01519656
## 66.66667% 0.04696595 0.02913048 0.1892978 0.4216657 0.01760980
## 100% 1.06086396 1.03590164 1.1943410 1.4610910 1.03090134
## rs4752566
## 0% -0.09730081
## 33.33333% 0.93805293
## 66.66667% 0.94677871
## 100% 1.96376129## Grouping limits, enhancer regions:## rs3750817 rs2981428 rs2912771 rs6659735 rs7138803
## 0% -0.3189679 -0.3189679 -0.3189679 -0.97485797 -0.2907022
## 33.33333% 0.8277747 0.8277747 0.8277747 0.05026514 0.8252121
## 66.66667% 0.8731637 0.8731637 0.8731637 0.06255916 0.8509063
## 100% 1.9519994 1.9519994 1.9519994 1.10194979 1.9117069
## rs713586
## 0% -0.7552842
## 33.33333% 0.5620456
## 66.66667% 0.6208045
## 100% 1.7606736## Grouping limits, gene regions:## rs4621895 rs1546124 rs3750817 rs2981428 rs9939609 rs6010718
## 0% -0.8062911 -0.3643344 -0.414893 -0.414893 -0.1791937 -0.4435039
## 33.33333% 0.2137940 0.6792211 0.636900 0.636900 0.8552454 0.5831739
## 66.66667% 0.2280363 0.6900403 0.651396 0.651396 0.8697097 0.5911365
## 100% 1.2849581 1.7102124 1.700709 1.700709 1.9295991 1.6105598
## rs3752462 rs2912771 rs6659735 rs10767664 rs4752566
## 0% -0.1462102 -0.2304825 -0.8767731 -0.94034857 -0.2435622
## 33.33333% 0.8698621 0.7936511 0.1359904 0.06741833 0.7799712
## 66.66667% 0.8732337 0.8030603 0.1424227 0.07064315 0.7871033
## 100% 1.8808361 1.8179549 1.1583152 1.07701203 1.8020110Running haplinStrat
Promoter regions
## Choosing the subset of data with only those individuals that we have methylation data for:## Provided arguments:
## --- argument: id, chosen values: 1, 5, 8, 11, 13, 15 ... 675, 676, 678, 682, 683, 684
## INFO: Will select 269 rows and 120 columns.## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmpq8aoPH/ff3d829105743.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: rs4621895 is in position: 2
## SNP for gene: rs1546124 is in position: 3
## SNP for gene: rs3750817 is in position: 4
## SNP for gene: rs2981428 is in position: 5
## SNP for gene: rs10984103 is in position: 6
## SNP for gene: rs9939609 is in position: 7
## SNP for gene: rs6010718 is in position: 8
## SNP for gene: rs3752462 is in position: 10
## SNP for gene: rs2867125 is in position: 11
## SNP for gene: rs2912771 is in position: 12
## SNP for gene: rs6659735 is in position: 13
## SNP for gene: rs10767664 is in position: 14
## SNP for gene: rs7138803 is in position: 15
## SNP for gene: rs713586 is in position: 17
## SNP for gene: rs1443433 is in position: 18
## SNP for gene: rs4752566 is in position: 19##
## HaplinStrat:## === GENE: rs4621895 ===
## 1. retrieving the subset of data:
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 269 rows and 6 columns.## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpQPJQtM/ff1c44bd295f.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:
## 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/RtmpQPJQtM/ff1c442d2532e.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/RtmpQPJQtM/ff1c44104b11d0.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"...## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.## Done
## === GENE: rs1546124 ===
## 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/RtmpQPJQtM/ff1c4471161b70.ff## ...done, all alleles: C 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/RtmpQPJQtM/ff1c4420a54cd1.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: rs3750817 ===
## 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/RtmpQPJQtM/ff1c4427166fe2.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/RtmpQPJQtM/ff1c4446894e4f.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: rs2981428 ===
## 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/RtmpQPJQtM/ff1c445dae1084.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/RtmpQPJQtM/ff1c443fbf2a89.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: rs10984103 ===
## 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/RtmpQPJQtM/ff1c444497796.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/RtmpQPJQtM/ff1c44372515f.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: rs9939609 ===
## 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/RtmpQPJQtM/ff1c4465421c1f.ff## ...done, all alleles: A 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/RtmpQPJQtM/ff1c44292f5cd5.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: rs6010718 ===
## 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_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/RtmpQPJQtM/ff1c442b522467.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/RtmpQPJQtM/ff1c4418621f94.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: rs3752462 ===
## 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/RtmpQPJQtM/ff1c443d1d687d.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/RtmpQPJQtM/ff1c4411d9368.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: rs2867125 ===
## 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/RtmpQPJQtM/ff1c44242f14b2.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/RtmpQPJQtM/ff1c441c127c3.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: rs2912771 ===
## 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/RtmpQPJQtM/ff1c4445c63c1c.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/RtmpQPJQtM/ff1c4457dc3038.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: rs6659735 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 13
## 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/RtmpQPJQtM/ff1c442b576b14.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/RtmpQPJQtM/ff1c447c017301.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: rs10767664 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 14
## 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/RtmpQPJQtM/ff1c441b0749b8.ff## ...done, all alleles: A 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/RtmpQPJQtM/ff1c44129a377a.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: rs7138803 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 15
## 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/RtmpQPJQtM/ff1c44334e69.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/RtmpQPJQtM/ff1c4411254a3.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: rs713586 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 17
## 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/RtmpQPJQtM/ff1c4423e94e.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/RtmpQPJQtM/ff1c4422b47fa2.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: rs1443433 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 18
## 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/RtmpQPJQtM/ff1c44356d49d0.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/RtmpQPJQtM/ff1c445c6d5a3f.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: rs4752566 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 19
## 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/RtmpQPJQtM/ff1c4422b55b1c.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/RtmpQPJQtM/ff1c44420a5167.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- plotting results:
gxetest:
## --- GENE: rs4621895 ---
## ------- GxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 4.327032 2 0.11492033
## 2 child 4.273024 2 0.11806593
## 3 haplo.freq.trend 4.306720 1 0.03796209
## 4 child.trend 3.901943 1 0.04823029
## ------- PoOxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 2.06509191 2 0.3560992
## 2 poo 0.63470992 2 0.7280723
## 3 haplo.freq.trend 0.86034624 1 0.3536418
## 4 poo.trend 0.01927854 1 0.8895709
## ------
## --- GENE: rs1546124 ---
## ------- GxM: rs1546124
## gxe.test chisq df pval
## 1 haplo.freq 2.831926 2 0.24269175
## 2 child 3.623136 2 0.16339770
## 3 haplo.freq.trend 2.470350 1 0.11601206
## 4 child.trend 3.051398 1 0.08066767
## ------- PoOxM: rs1546124
## gxe.test chisq df pval
## 1 haplo.freq 3.6528764 2 0.1609859
## 2 poo 1.2419425 2 0.5374222
## 3 haplo.freq.trend 2.6122928 1 0.1060384
## 4 poo.trend 0.1727958 1 0.6776390
## ------
## --- GENE: rs3750817 ---
## ------- GxM: rs3750817
## gxe.test chisq df pval
## 1 haplo.freq 0.6751518 2 0.7134978
## 2 child 1.0638390 2 0.5874762
## 3 haplo.freq.trend 0.0213802 1 0.8837480
## 4 child.trend 0.2625397 1 0.6083807
## ------- PoOxM: rs3750817
## gxe.test chisq df pval
## 1 haplo.freq 0.9169749 2 0.6322392
## 2 poo 1.1458165 2 0.5638831
## 3 haplo.freq.trend 0.4829879 1 0.4870720
## 4 poo.trend 1.1445409 1 0.2846948
## ------
## --- GENE: rs2981428 ---
## ------- GxM: rs2981428
## gxe.test chisq df pval
## 1 haplo.freq 0.74985406 2 0.6873394
## 2 child 1.42874333 2 0.4894996
## 3 haplo.freq.trend 0.07472605 1 0.7845760
## 4 child.trend 0.05290697 1 0.8180800
## ------- PoOxM: rs2981428
## gxe.test chisq df pval
## 1 haplo.freq 0.95797865 2 0.6194091
## 2 poo 0.34326829 2 0.8422873
## 3 haplo.freq.trend 0.04849929 1 0.8256955
## 4 poo.trend 0.01776755 1 0.8939601
## ------
## --- GENE: rs10984103 ---
## ------- GxM: rs10984103
## gxe.test chisq df pval
## 1 haplo.freq 0.0066403378 2 0.9966853
## 2 child 0.0251942268 2 0.9874819
## 3 haplo.freq.trend 0.0002866479 1 0.9864919
## 4 child.trend 0.0093873537 1 0.9228151
## ------- PoOxM: rs10984103
## gxe.test chisq df pval
## 1 haplo.freq 2.356732 2 0.307781175
## 2 poo 9.198650 2 0.010058622
## 3 haplo.freq.trend 2.177347 1 0.140055713
## 4 poo.trend 8.788632 1 0.003031135
## ------
## --- GENE: rs9939609 ---
## ------- GxM: rs9939609
## gxe.test chisq df pval
## 1 haplo.freq 3.63496010 2 0.1624346
## 2 child 2.71385561 2 0.2574505
## 3 haplo.freq.trend 0.06773899 1 0.7946577
## 4 child.trend 0.01576625 1 0.9000773
## ------- PoOxM: rs9939609
## gxe.test chisq df pval
## 1 haplo.freq 1.5722796 2 0.4556001
## 2 poo 3.1045413 2 0.2117666
## 3 haplo.freq.trend 1.3363192 1 0.2476841
## 4 poo.trend 0.7529827 1 0.3855335
## ------
## --- GENE: rs6010718 ---
## ------- GxM: rs6010718
## gxe.test chisq df pval
## 1 haplo.freq 2.42757157 2 0.2970705
## 2 child 0.05858541 2 0.9711322
## 3 haplo.freq.trend 2.31584984 1 0.1280613
## 4 child.trend 0.03445622 1 0.8527397
## ------- PoOxM: rs6010718
## gxe.test chisq df pval
## 1 haplo.freq 1.96265171 2 0.3748138
## 2 poo 2.14809037 2 0.3416238
## 3 haplo.freq.trend 1.96178168 1 0.1613229
## 4 poo.trend 0.09497572 1 0.7579444
## ------
## --- GENE: rs3752462 ---
## ------- GxM: rs3752462
## gxe.test chisq df pval
## 1 haplo.freq 0.069245173 2 0.9659699
## 2 child 0.491862977 2 0.7819758
## 3 haplo.freq.trend 0.001753243 1 0.9666009
## 4 child.trend 0.487267286 1 0.4851488
## ------- PoOxM: rs3752462
## gxe.test chisq df pval
## 1 haplo.freq 3.7510136 2 0.15327726
## 2 poo 5.9399173 2 0.05130543
## 3 haplo.freq.trend 1.4183991 1 0.23366709
## 4 poo.trend 0.9327098 1 0.33415979
## ------
## --- GENE: rs2867125 ---
## ------- GxM: rs2867125
## gxe.test chisq df pval
## 1 haplo.freq 0.654765889 2 0.7208077
## 2 child 0.798372319 2 0.6708658
## 3 haplo.freq.trend 0.019636112 1 0.8885581
## 4 child.trend 0.008319016 1 0.9273268
## ------- PoOxM: rs2867125
## gxe.test chisq df pval
## 1 haplo.freq 0.9430649 2 0.6240452
## 2 poo 0.9567130 2 0.6198012
## 3 haplo.freq.trend 0.1727243 1 0.6777019
## 4 poo.trend 0.8634636 1 0.3527712
## ------
## --- GENE: rs2912771 ---
## ------- GxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 0.018121388 2 0.9909802
## 2 child 0.027054730 2 0.9865637
## 3 haplo.freq.trend 0.004640081 1 0.9456916
## 4 child.trend 0.024231820 1 0.8762965
## ------- PoOxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 1.356192 2 0.50758247
## 2 poo 5.471821 2 0.06483495
## 3 haplo.freq.trend 1.242629 1 0.26496507
## 4 poo.trend 5.467395 1 0.01937449
## ------
## --- GENE: rs6659735 ---
## ------- GxM: rs6659735
## gxe.test chisq df pval
## 1 haplo.freq 0.28240742 2 0.8683124
## 2 child 0.71083863 2 0.7008795
## 3 haplo.freq.trend 0.25618066 1 0.6127563
## 4 child.trend 0.02191004 1 0.8823267
## ------- PoOxM: rs6659735
## gxe.test chisq df pval
## 1 haplo.freq 0.011355148 2 0.9943385
## 2 poo 0.978691862 2 0.6130272
## 3 haplo.freq.trend 0.000925368 1 0.9757322
## 4 poo.trend 0.328706342 1 0.5664218
## ------
## --- GENE: rs10767664 ---
## ------- GxM: rs10767664
## gxe.test chisq df pval
## 1 haplo.freq 5.7518886 2 0.05636289
## 2 child 2.8089182 2 0.24549981
## 3 haplo.freq.trend 4.5927061 1 0.03210828
## 4 child.trend 0.5908843 1 0.44207735
## ------- PoOxM: rs10767664
## gxe.test chisq df pval
## 1 haplo.freq 4.5425755 2 0.10317923
## 2 poo 0.6960207 2 0.70609158
## 3 haplo.freq.trend 2.7274738 1 0.09863519
## 4 poo.trend 0.2536380 1 0.61452499
## ------
## --- GENE: rs7138803 ---
## ------- GxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 3.339572 2 0.1882874
## 2 child 4.465864 2 0.1072136
## 3 haplo.freq.trend 1.433851 1 0.2311369
## 4 child.trend 2.092049 1 0.1480674
## ------- PoOxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 5.2134826 2 0.07377456
## 2 poo 7.4856753 2 0.02368679
## 3 haplo.freq.trend 0.4671686 1 0.49429262
## 4 poo.trend 5.9264914 1 0.01491491
## ------
## --- GENE: rs713586 ---
## ------- GxM: rs713586
## gxe.test chisq df pval
## 1 haplo.freq 3.0979436 2 0.2124663
## 2 child 4.3342382 2 0.1145070
## 3 haplo.freq.trend 1.1808516 1 0.2771827
## 4 child.trend 0.2716806 1 0.6022066
## ------- PoOxM: rs713586
## gxe.test chisq df pval
## 1 haplo.freq 3.33264190 2 0.1889409
## 2 poo 1.97341523 2 0.3728021
## 3 haplo.freq.trend 0.02755548 1 0.8681582
## 4 poo.trend 0.97558197 1 0.3232920
## ------
## --- GENE: rs1443433 ---
## ------- GxM: rs1443433
## gxe.test chisq df pval
## 1 haplo.freq 1.40714324 2 0.4948149
## 2 child 0.90209460 2 0.6369607
## 3 haplo.freq.trend 0.41550939 1 0.5191863
## 4 child.trend 0.06811979 1 0.7940943
## ------- PoOxM: rs1443433
## gxe.test chisq df pval
## 1 haplo.freq 1.0189595 2 0.6008081
## 2 poo 2.5235097 2 0.2831567
## 3 haplo.freq.trend 0.6601627 1 0.4165025
## 4 poo.trend 0.6842828 1 0.4081158
## ------
## --- GENE: rs4752566 ---
## ------- GxM: rs4752566
## gxe.test chisq df pval
## 1 haplo.freq 1.361107 2 0.5063366
## 2 child 1.200533 2 0.5486655
## 3 haplo.freq.trend 1.325037 1 0.2496900
## 4 child.trend 1.143678 1 0.2848765
## ------- PoOxM: rs4752566
## gxe.test chisq df pval
## 1 haplo.freq 0.28969334 2 0.86515494
## 2 poo 3.09328082 2 0.21296224
## 3 haplo.freq.trend 0.06134977 1 0.80437515
## 4 poo.trend 2.76101317 1 0.09658705
## ------Enhancer regions
## Choosing the subset of data with only those individuals that we have methylation data for:## Provided arguments:
## --- argument: id, chosen values: 1, 5, 8, 11, 13, 15 ... 675, 676, 678, 682, 683, 684
## INFO: Will select 269 rows and 120 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: rs3750817 is in position: 4
## SNP for gene: rs2981428 is in position: 5
## SNP for gene: rs2912771 is in position: 12
## SNP for gene: rs6659735 is in position: 13
## SNP for gene: rs7138803 is in position: 15
## SNP for gene: rs713586 is in position: 17##
## HaplinStrat:## === GENE: rs3750817 ===
## 1. retrieving the subset of data:
## Provided arguments:
## --- chosen markers: 4
## INFO: Will select 269 rows and 6 columns.## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpQPJQtM/ff1c441a5a3ba9.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:
## 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/RtmpQPJQtM/ff1c441b725a4a.ff## ...done, all alleles: C 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/RtmpQPJQtM/ff1c44677af5c.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: rs2981428 ===
## 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_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/RtmpQPJQtM/ff1c44223d79.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/RtmpQPJQtM/ff1c441a7011de.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: rs2912771 ===
## 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_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/RtmpQPJQtM/ff1c4458c626c3.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/RtmpQPJQtM/ff1c4417c82221.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: rs6659735 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 13
## 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/RtmpQPJQtM/ff1c44478d5998.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/RtmpQPJQtM/ff1c4412f1792a.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: rs7138803 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 15
## 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/RtmpQPJQtM/ff1c44201304a.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/RtmpQPJQtM/ff1c44618f1f43.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"...## 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: rs713586 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 17
## 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/RtmpQPJQtM/ff1c44137e728f.ff## ...done, all alleles: C 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/RtmpQPJQtM/ff1c4453f94e79.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- plotting results:
gxetest:
## --- GENE: rs3750817 ---
## ------- GxM: rs3750817
## gxe.test chisq df pval
## 1 haplo.freq 0.5955081 2 0.7424839
## 2 child 0.4247454 2 0.8086633
## 3 haplo.freq.trend 0.1436706 1 0.7046589
## 4 child.trend 0.3425938 1 0.5583359
## ------- PoOxM: rs3750817
## gxe.test chisq df pval
## 1 haplo.freq 0.04236816 2 0.9790387
## 2 poo 1.89210300 2 0.3882711
## 3 haplo.freq.trend 0.04210321 1 0.8374232
## 4 poo.trend 0.03234045 1 0.8572825
## ------
## --- GENE: rs2981428 ---
## ------- GxM: rs2981428
## gxe.test chisq df pval
## 1 haplo.freq 0.545978071 2 0.7611011
## 2 child 0.170956887 2 0.9180729
## 3 haplo.freq.trend 0.007798415 1 0.9296314
## 4 child.trend 0.053093595 1 0.8177651
## ------- PoOxM: rs2981428
## gxe.test chisq df pval
## 1 haplo.freq 0.33357753 2 0.8463784
## 2 poo 0.29008535 2 0.8649854
## 3 haplo.freq.trend 0.01811339 1 0.8929392
## 4 poo.trend 0.23757184 1 0.6259654
## ------
## --- GENE: rs2912771 ---
## ------- GxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 0.715974496 2 0.6990820
## 2 child 0.094329047 2 0.9539304
## 3 haplo.freq.trend 0.438065200 1 0.5080578
## 4 child.trend 0.006570458 1 0.9353955
## ------- PoOxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 1.188140617 2 0.5520756
## 2 poo 1.146164664 2 0.5637850
## 3 haplo.freq.trend 0.002491495 1 0.9601902
## 4 poo.trend 0.213353240 1 0.6441518
## ------
## --- GENE: rs6659735 ---
## ------- GxM: rs6659735
## gxe.test chisq df pval
## 1 haplo.freq 4.6245651 2 0.09903494
## 2 child 1.4126450 2 0.49345554
## 3 haplo.freq.trend 0.7259154 1 0.39421039
## 4 child.trend 0.4712663 1 0.49240520
## ------- PoOxM: rs6659735
## gxe.test chisq df pval
## 1 haplo.freq 2.512737638 2 0.2846859
## 2 poo 0.903757052 2 0.6364315
## 3 haplo.freq.trend 0.618973158 1 0.4314291
## 4 poo.trend 0.005356139 1 0.9416584
## ------
## --- GENE: rs7138803 ---
## ------- GxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 0.2972426 2 0.8618954
## 2 child 0.3103363 2 0.8562712
## 3 haplo.freq.trend 0.2347169 1 0.6280481
## 4 child.trend 0.1543814 1 0.6943831
## ------- PoOxM: rs7138803
## gxe.test chisq df pval
## 1 haplo.freq 0.8812835 2 0.6436232
## 2 poo 1.2813728 2 0.5269306
## 3 haplo.freq.trend 0.3476290 1 0.5554584
## 4 poo.trend 0.1024671 1 0.7488888
## ------
## --- GENE: rs713586 ---
## ------- GxM: rs713586
## gxe.test chisq df pval
## 1 haplo.freq 2.304039 2 0.3159979
## 2 child 2.268466 2 0.3216688
## 3 haplo.freq.trend 2.234571 1 0.1349540
## 4 child.trend 2.253835 1 0.1332838
## ------- PoOxM: rs713586
## gxe.test chisq df pval
## 1 haplo.freq 1.8070553 2 0.4051380
## 2 poo 2.8843031 2 0.2364185
## 3 haplo.freq.trend 0.6938796 1 0.4048479
## 4 poo.trend 0.4906538 1 0.4836358
## ------Gene regions
## Choosing the subset of data with only those individuals that we have methylation data for:## Provided arguments:
## --- argument: id, chosen values: 1, 5, 8, 11, 13, 15 ... 675, 676, 678, 682, 683, 684
## INFO: Will select 269 rows and 120 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: rs4621895 is in position: 2
## SNP for gene: rs1546124 is in position: 3
## SNP for gene: rs3750817 is in position: 4
## SNP for gene: rs2981428 is in position: 5
## SNP for gene: rs9939609 is in position: 7
## SNP for gene: rs6010718 is in position: 8
## SNP for gene: rs3752462 is in position: 10
## SNP for gene: rs2912771 is in position: 12
## SNP for gene: rs6659735 is in position: 13
## SNP for gene: rs10767664 is in position: 14
## SNP for gene: rs4752566 is in position: 19##
## HaplinStrat:## === GENE: rs4621895 ===
## 1. retrieving the subset of data:
## Provided arguments:
## --- chosen markers: 2
## INFO: Will select 269 rows and 6 columns.## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpQPJQtM/ff1c445db9651f.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:
## 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/RtmpQPJQtM/ff1c4432807551.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/RtmpQPJQtM/ff1c4426974e39.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"...## Warning: Maximum number of EM iterations reached!
## Convergence not yet obtained. Setting max.EM.iter higher may help.## Done
## === GENE: rs1546124 ===
## 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/RtmpQPJQtM/ff1c443bd926f6.ff## ...done, all alleles: C 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/RtmpQPJQtM/ff1c44597a7b4d.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: rs3750817 ===
## 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/RtmpQPJQtM/ff1c445997bc5.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/RtmpQPJQtM/ff1c44470c6ee7.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: rs2981428 ===
## 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_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/RtmpQPJQtM/ff1c44221c91d.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/RtmpQPJQtM/ff1c4438e35157.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: rs9939609 ===
## 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/RtmpQPJQtM/ff1c44713d47e3.ff## ...done, all alleles: A 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/RtmpQPJQtM/ff1c441fe56dcf.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: rs6010718 ===
## 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/RtmpQPJQtM/ff1c4448c33efe.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/RtmpQPJQtM/ff1c4460cf18e5.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: rs3752462 ===
## 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/RtmpQPJQtM/ff1c44ea4dda.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/RtmpQPJQtM/ff1c4470b22715.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: rs2912771 ===
## 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/RtmpQPJQtM/ff1c4448e566e6.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/RtmpQPJQtM/ff1c444171733d.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: rs6659735 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 13
## 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/RtmpQPJQtM/ff1c4477584a16.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/RtmpQPJQtM/ff1c447e44751f.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: rs10767664 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 14
## 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/RtmpQPJQtM/ff1c442adc4f61.ff## ...done, all alleles: A 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/RtmpQPJQtM/ff1c44183867e2.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: rs4752566 ===
## 1. retrieving the subset of data:
## The output file(s) exist!
## Provided arguments:
## --- chosen markers: 19
## 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/RtmpQPJQtM/ff1c443a7f4144.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/RtmpQPJQtM/ff1c4422ad91.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"...## 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- plotting results:
gxetest:
## --- GENE: rs4621895 ---
## ------- GxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 3.655064 2 0.16080994
## 2 child 3.327708 2 0.18940757
## 3 haplo.freq.trend 3.629263 1 0.05677196
## 4 child.trend 3.325446 1 0.06821550
## ------- PoOxM: rs4621895
## gxe.test chisq df pval
## 1 haplo.freq 0.92985116 2 0.6281819
## 2 poo 0.15787430 2 0.9240980
## 3 haplo.freq.trend 0.58187733 1 0.4455774
## 4 poo.trend 0.04957988 1 0.8237959
## ------
## --- GENE: rs1546124 ---
## ------- GxM: rs1546124
## gxe.test chisq df pval
## 1 haplo.freq 5.817311 2 0.05454902
## 2 child 2.698475 2 0.25943800
## 3 haplo.freq.trend 5.637577 1 0.01757949
## 4 child.trend 2.635928 1 0.10447103
## ------- PoOxM: rs1546124
## gxe.test chisq df pval
## 1 haplo.freq 3.5668231 2 0.16806381
## 2 poo 1.2110638 2 0.54578404
## 3 haplo.freq.trend 3.5543521 1 0.05938949
## 4 poo.trend 0.4807458 1 0.48808472
## ------
## --- GENE: rs3750817 ---
## ------- GxM: rs3750817
## gxe.test chisq df pval
## 1 haplo.freq 0.3643558 2 0.8334530
## 2 child 0.2522788 2 0.8814919
## 3 haplo.freq.trend 0.1072349 1 0.7433144
## 4 child.trend 0.2294305 1 0.6319465
## ------- PoOxM: rs3750817
## gxe.test chisq df pval
## 1 haplo.freq 1.7085987 2 0.4255813
## 2 poo 4.3984907 2 0.1108868
## 3 haplo.freq.trend 0.1460817 1 0.7023083
## 4 poo.trend 1.9115200 1 0.1667945
## ------
## --- GENE: rs2981428 ---
## ------- GxM: rs2981428
## gxe.test chisq df pval
## 1 haplo.freq 0.155191344 2 0.9253385
## 2 child 0.313589551 2 0.8548795
## 3 haplo.freq.trend 0.001352267 1 0.9706659
## 4 child.trend 0.021017850 1 0.8847303
## ------- PoOxM: rs2981428
## gxe.test chisq df pval
## 1 haplo.freq 1.6363339 2 0.44123972
## 2 poo 5.5212206 2 0.06325315
## 3 haplo.freq.trend 0.2499654 1 0.61709946
## 4 poo.trend 1.5524244 1 0.21277789
## ------
## --- GENE: rs9939609 ---
## ------- GxM: rs9939609
## gxe.test chisq df pval
## 1 haplo.freq 0.3695328 2 0.8312984
## 2 child 2.5603298 2 0.2779915
## 3 haplo.freq.trend 0.0248704 1 0.8746904
## 4 child.trend 0.8060865 1 0.3692798
## ------- PoOxM: rs9939609
## gxe.test chisq df pval
## 1 haplo.freq 2.349260 2 0.30893323
## 2 poo 3.134072 2 0.20866275
## 3 haplo.freq.trend 1.798379 1 0.17990862
## 4 poo.trend 3.083202 1 0.07910466
## ------
## --- GENE: rs6010718 ---
## ------- GxM: rs6010718
## gxe.test chisq df pval
## 1 haplo.freq 3.4000514 2 0.1826788
## 2 child 1.0062677 2 0.6046329
## 3 haplo.freq.trend 2.5123902 1 0.1129545
## 4 child.trend 0.8808623 1 0.3479656
## ------- PoOxM: rs6010718
## gxe.test chisq df pval
## 1 haplo.freq 3.2452948 2 0.1973755
## 2 poo 0.7083853 2 0.7017398
## 3 haplo.freq.trend 2.1628265 1 0.1413844
## 4 poo.trend 0.4919264 1 0.4830692
## ------
## --- GENE: rs3752462 ---
## ------- GxM: rs3752462
## gxe.test chisq df pval
## 1 haplo.freq 2.3630639 2 0.30680837
## 2 child 4.7558530 2 0.09274268
## 3 haplo.freq.trend 0.2755685 1 0.59962060
## 4 child.trend 0.7055934 1 0.40091059
## ------- PoOxM: rs3752462
## gxe.test chisq df pval
## 1 haplo.freq 0.396831208 2 0.8200290
## 2 poo 1.798589118 2 0.4068566
## 3 haplo.freq.trend 0.325405098 1 0.5683773
## 4 poo.trend 0.006619204 1 0.9351569
## ------
## --- GENE: rs2912771 ---
## ------- GxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 0.9089409 2 0.6347840
## 2 child 2.2153613 2 0.3303242
## 3 haplo.freq.trend 0.1673054 1 0.6825178
## 4 child.trend 0.7451187 1 0.3880261
## ------- PoOxM: rs2912771
## gxe.test chisq df pval
## 1 haplo.freq 1.2355270 2 0.5391489
## 2 poo 0.9651973 2 0.6171775
## 3 haplo.freq.trend 0.9445006 1 0.3311231
## 4 poo.trend 0.9434837 1 0.3313835
## ------
## --- GENE: rs6659735 ---
## ------- GxM: rs6659735
## gxe.test chisq df pval
## 1 haplo.freq 0.5048555 2 0.7769123
## 2 child 0.4612540 2 0.7940356
## 3 haplo.freq.trend 0.2729371 1 0.6013683
## 4 child.trend 0.4249161 1 0.5144942
## ------- PoOxM: rs6659735
## gxe.test chisq df pval
## 1 haplo.freq 0.19920747 2 0.9051960
## 2 poo 0.15456227 2 0.9256296
## 3 haplo.freq.trend 0.15645782 1 0.6924389
## 4 poo.trend 0.02950126 1 0.8636268
## ------
## --- GENE: rs10767664 ---
## ------- GxM: rs10767664
## gxe.test chisq df pval
## 1 haplo.freq 2.428185 2 0.29697936
## 2 child 5.100049 2 0.07807974
## 3 haplo.freq.trend 2.412920 1 0.12033769
## 4 child.trend 4.865511 1 0.02739869
## ------- PoOxM: rs10767664
## gxe.test chisq df pval
## 1 haplo.freq 2.7496153 2 0.25288823
## 2 poo 0.8935775 2 0.63967902
## 3 haplo.freq.trend 2.7384592 1 0.09795918
## 4 poo.trend 0.5301704 1 0.46653524
## ------
## --- GENE: rs4752566 ---
## ------- GxM: rs4752566
## gxe.test chisq df pval
## 1 haplo.freq 0.8233931 2 0.6625253
## 2 child 0.6000684 2 0.7407929
## 3 haplo.freq.trend 0.6019676 1 0.4378283
## 4 child.trend 0.2180114 1 0.6405593
## ------- PoOxM: rs4752566
## gxe.test chisq df pval
## 1 haplo.freq 0.4053591 2 0.8165398
## 2 poo 0.2089036 2 0.9008182
## 3 haplo.freq.trend 0.1551520 1 0.6936598
## 4 poo.trend 0.1699489 1 0.6801573
## ------## Saved image to file: GxM_PoOxM_new_betas_mult_randomSNPs_ CLorP .RData