Introduction

I chose those SNPs (from Moreno et al., 2017):

##    Chr    snpname      pos1      pos2 gene_name
## 1    1   rs742071  18979874  18979875      PAX7
## 2    1   rs560426  94553438  94553439     ABCA4
## 3    1   rs642961 209989270 209989271      IRF6
## 4    2  rs7590268  43540125  43540126     THADA
## 5    8 rs12543318  88868340  88868341    8q21.3
## 6    8   rs987525 129946154 129946155      8q24
## 7    9  rs3758249 100614140 100614141     FOXE1
## 8   10  rs7078160 118827560 118827561  KIAA1598
## 9   13  rs8001641  80692811  80692812     SPRY2
## 10  15  rs1873147  63312632  63312633      TPM1
## 11  17   rs227731  54773238  54773239      NOG1
## 12  20 rs13041247  39269074  39269075      MAFB

NOTE: all the genome positions here are from build hg19!

These analyses are for cleft type CLP!

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:
##      PAX7 ABCA4 IRF6 THADA 8q21.3 8q24 FOXE1 SPRY2 TPM1 NOG1 MAFB
## [1,]  166   166  166   166    166  166   166   166  166  166  166
## [2,]   19     1   14     1      1    1     6     1   30    2   21
  1. for the enhancer region:
##      PAX7 ABCA4 THADA 8q24 KIAA1598 SPRY2
## [1,]  166   166   166  166      166   166
## [2,]    1     6     1    1        1     1
  1. for the gene region:
##      PAX7 ABCA4 IRF6 THADA FOXE1 KIAA1598 TPM1 MAFB
## [1,]  166   166  166   166   166      166  166  166
## [2,]   54    16   27    14     7        1   29    9

Categorizing methylation values

Divide the individuals in three groups (created by calculating the 33% and 66% quantiles)

## Grouping limits, promoter regions:
##                  PAX7      ABCA4       IRF6       THADA      8q21.3
## 0%        -0.96691483 -0.1244538 -0.9040936 -0.06567031 -0.04889268
## 33.33333%  0.04258831  0.9359239  0.1208876  0.95868248  0.97115570
## 66.66667%  0.04723040  0.9494929  0.1372878  0.96535248  0.97441041
## 100%       1.06086396  1.9705125  1.1947128  1.97611719  1.98632121
##                 8q24       FOXE1       SPRY2       TPM1       NOG1
## 0%        -0.6060226 -0.98794349 -0.04859895 -0.7814193 -0.5120293
## 33.33333%  0.7508203  0.01542281  0.97459638  0.2376595  0.5118647
## 66.66667%  0.8244217  0.01756489  0.97844535  0.2465935  0.5221919
## 100%       1.9248418  1.03090134  1.98594815  1.2709067  1.5579287
##                  MAFB
## 0%        -0.94198720
## 33.33333%  0.07215136
## 66.66667%  0.07924527
## 100%       1.09590999
## Grouping limits, enhancer regions:
##                  PAX7       ABCA4       THADA        8q24    KIAA1598
## 0%        -0.97289033 -0.06776287 -0.03621757 -0.05056983 -0.05018514
## 33.33333%  0.05056198  0.94623069  0.97658700  0.96851492  0.97082043
## 66.66667%  0.06311021  0.95026225  0.97945350  0.97285628  0.97487551
## 100%       1.10194979  1.95850337  1.98461539  1.98034143  1.98267764
##                SPRY2
## 0%        -0.2352023
## 33.33333%  0.8727414
## 66.66667%  0.8990984
## 100%       1.9566071
## Grouping limits, gene regions:
##                 PAX7      ABCA4       IRF6      THADA       FOXE1
## 0%        -0.8911824 -0.2447756 -0.5730036 -0.1540526 -0.94472579
## 33.33333%  0.1217193  0.8016359  0.4405855  0.8894449  0.07450210
## 66.66667%  0.1279638  0.8100850  0.4440570  0.9058691  0.08358899
## 100%       1.1436416  1.8333790  1.4520446  1.9464645  1.10222436
##              KIAA1598       TPM1        MAFB
## 0%        -0.05018514 -0.5312118 -0.96281233
## 33.33333%  0.97082043  0.4867602  0.05040960
## 66.66667%  0.97487551  0.4929923  0.05573132
## 100%       1.98267764  1.5007956  1.07272602

Running haplinStrat

Promoter regions

## Choosing the subset of data with only those individuals that we have methylation data for:
## The output file(s) exist! 
## Provided arguments:
##  --- argument: id, chosen values: 1, 5, 8, 13, 15, 19 ... 671, 672, 675, 682, 683, 684
## INFO: Will select 166 rows and 72 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/Rtmpq6iF6H/ff4c44ce71911.ff
## Saving data... 
## ... saved to files: ./data_subset_promoter_GxM_gen.ffData, ./data_subset_promoter_GxM_gen.RData
## Check which SNPs are in the current dataset:
##   SNP for gene:  PAX7  is in position:  1 
##   SNP for gene:  ABCA4  is in position:  2 
##   SNP for gene:  IRF6  is in position:  3 
##   SNP for gene:  THADA  is in position:  4 
##   SNP for gene:  8q21.3  is in position:  5 
##   SNP for gene:  8q24  is in position:  6 
##   SNP for gene:  FOXE1  is in position:  7 
##   SNP for gene:  SPRY2  is in position:  9 
##   SNP for gene:  TPM1  is in position:  10 
##   SNP for gene:  NOG1  is in position:  11 
##   SNP for gene:  MAFB  is in position:  12
## 
##  HaplinStrat:
## === GENE:  PAX7  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 1 
## INFO: Will select 166 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b78560771ab.ff
## Saving data... 
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
##   2. adding strata information and preprocessing data:
## The output file(s) exist! 
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
##    ...running on only one CPU core! This may take some time...
##    ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7840616082.ff
##    ...done, all alleles: G T 
##    ...recoding SNPs...
##    ...done
## Saving data... 
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData ,  ./data_subset3_promoter_GxM_gen.RData 
##   3. running haplinStrat:
##      3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7811a02db1.ff
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## 
##      3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## === GENE:  ABCA4  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 2 
## INFO: Will select 166 rows and 6 columns.
## Saving data... 
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
##   2. adding strata information and preprocessing data:
## The output file(s) exist! 
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
##    ...running on only one CPU core! This may take some time...
##    ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b785f663a64.ff
##    ...done, all alleles: A G 
##    ...recoding SNPs...
##    ...done
## Saving data... 
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData ,  ./data_subset3_promoter_GxM_gen.RData 
##   3. running haplinStrat:
##      3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b78208d108a.ff
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## 
##      3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## === GENE:  IRF6  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 3 
## INFO: Will select 166 rows and 6 columns.
## Saving data... 
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
##   2. adding strata information and preprocessing data:
## The output file(s) exist! 
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
##    ...running on only one CPU core! This may take some time...
##    ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b782835409.ff
##    ...done, all alleles: A G 
##    ...recoding SNPs...
##    ...done
## Saving data... 
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData ,  ./data_subset3_promoter_GxM_gen.RData 
##   3. running haplinStrat:
##      3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b783c80525c.ff
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## 
##      3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## === GENE:  THADA  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 4 
## INFO: Will select 166 rows and 6 columns.
## Saving data... 
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
##   2. adding strata information and preprocessing data:
## The output file(s) exist! 
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
##    ...running on only one CPU core! This may take some time...
##    ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b784d202381.ff
##    ...done, all alleles: G T 
##    ...recoding SNPs...
##    ...done
## Saving data... 
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData ,  ./data_subset3_promoter_GxM_gen.RData 
##   3. running haplinStrat:
##      3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7855c3333a.ff
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## 
##      3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## === GENE:  8q21.3  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 5 
## INFO: Will select 166 rows and 6 columns.
## Saving data... 
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
##   2. adding strata information and preprocessing data:
## The output file(s) exist! 
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
##    ...running on only one CPU core! This may take some time...
##    ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b783de050e.ff
##    ...done, all alleles: A C 
##    ...recoding SNPs...
##    ...done
## Saving data... 
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData ,  ./data_subset3_promoter_GxM_gen.RData 
##   3. running haplinStrat:
##      3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b78e637d4a.ff
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## 
##      3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## === GENE:  8q24  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 6 
## INFO: Will select 166 rows and 6 columns.
## Saving data... 
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
##   2. adding strata information and preprocessing data:
## The output file(s) exist! 
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
##    ...running on only one CPU core! This may take some time...
##    ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b781e0e73a7.ff
##    ...done, all alleles: A C 
##    ...recoding SNPs...
##    ...done
## Saving data... 
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData ,  ./data_subset3_promoter_GxM_gen.RData 
##   3. running haplinStrat:
##      3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b782cb3946.ff
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## 
##      3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## === GENE:  FOXE1  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 7 
## INFO: Will select 166 rows and 6 columns.
## Saving data... 
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
##   2. adding strata information and preprocessing data:
## The output file(s) exist! 
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
##    ...running on only one CPU core! This may take some time...
##    ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b784ba84178.ff
##    ...done, all alleles: C T 
##    ...recoding SNPs...
##    ...done
## Saving data... 
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData ,  ./data_subset3_promoter_GxM_gen.RData 
##   3. running haplinStrat:
##      3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b781dc712fd.ff
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## 
##      3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## === GENE:  SPRY2  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 9 
## INFO: Will select 166 rows and 6 columns.
## Saving data... 
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
##   2. adding strata information and preprocessing data:
## The output file(s) exist! 
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
##    ...running on only one CPU core! This may take some time...
##    ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b7875924060.ff
##    ...done, all alleles: A G 
##    ...recoding SNPs...
##    ...done
## Saving data... 
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData ,  ./data_subset3_promoter_GxM_gen.RData 
##   3. running haplinStrat:
##      3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b787f95dd1.ff
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## 
##      3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## === GENE:  TPM1  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 10 
## INFO: Will select 166 rows and 6 columns.
## Saving data... 
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
##   2. adding strata information and preprocessing data:
## The output file(s) exist! 
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
##    ...running on only one CPU core! This may take some time...
##    ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b784213a72.ff
##    ...done, all alleles: A G 
##    ...recoding SNPs...
##    ...done
## Saving data... 
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData ,  ./data_subset3_promoter_GxM_gen.RData 
##   3. running haplinStrat:
##      3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b786d682937.ff
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## 
##      3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## === GENE:  NOG1  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 11 
## INFO: Will select 166 rows and 6 columns.
## Saving data... 
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
##   2. adding strata information and preprocessing data:
## The output file(s) exist! 
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
##    ...running on only one CPU core! This may take some time...
##    ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b785541a75.ff
##    ...done, all alleles: G T 
##    ...recoding SNPs...
##    ...done
## Saving data... 
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData ,  ./data_subset3_promoter_GxM_gen.RData 
##   3. running haplinStrat:
##      3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b785e74753a.ff
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## 
##      3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## === GENE:  MAFB  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 12 
## INFO: Will select 166 rows and 6 columns.
## Saving data... 
## ... saved to files: ./data_subset2_promoter_GxM_gen.ffData, ./data_subset2_promoter_GxM_gen.RData
##   2. adding strata information and preprocessing data:
## The output file(s) exist! 
## Reading the marker names...
## Warning: No map file given or map file empty; will generate dummy marker
## names.
## ...done
## Recoding covariate data...
## ...done
## Recoding genetic data (no. of loci: 1)...
##    ...running on only one CPU core! This may take some time...
##    ...checking alleles per SNP...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b787e43465.ff
##    ...done, all alleles: C T 
##    ...recoding SNPs...
##    ...done
## Saving data... 
## ... saved to files: ./data_subset3_promoter_GxM_gen.ffData ,  ./data_subset3_promoter_GxM_gen.RData 
##   3. running haplinStrat:
##      3a. GxM
## Warning: response = "mult" must be used with reference category ( numeric
## or "ref.cat" ). Has been changed to reference = "ref.cat"
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpAzMhD1/ff1b783c4316f8.ff
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## 
##      3b. PoOxM
## Warning: Can only (for the time being) use reference = "ref.cat" or
## "population" when poo == TRUE. Has been changed to "ref.cat".
## 
## ## Running haplinStrat ##
## 
## Selected stratification variable: group.c
## Frequency distribution of stratification variable:
##  1  2  3 
## 56 55 55 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
  • plotting results: