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:

  1. identification of promoter and enhancer regions around the chosen SNPs, based on the regulatory ensembl database (build 37),
  2. extracting the matching data from both datasets, genomic and methylation

This gives the following data dimensions:

  1. 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
  1. for the enhancer region:
##      rs3750817 rs2981428 rs2912771 rs6659735 rs7138803 rs713586
## [1,]       269       269       269       269       269      269
## [2,]         1         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        21

Categorizing methylation 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  1.8020110

Running 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: