Introduction

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

##    no     marker                 haplotype       RRR RRR.lower RRR.upper
## 1   1    rs29941 a (39.6%), ref: G (60.4%) 0.5661675 0.3958836 0.8166947
## 2   2  rs2235371  t (5.7%), ref: C (94.3%) 2.3882332 1.2754485 4.3470971
## 3   3  rs4752028 c (22.8%), ref: T (77.2%) 0.7062425 0.5235802 0.9566427
## 4   4   rs633265 t (40.8%), ref: G (59.2%) 0.7236589 0.5211402 0.9914430
## 5   5  rs2912760 t (29.4%), ref: G (70.6%) 0.7332222 0.5328104 0.9955550
## 6   6 rs11084753 a (37.7%), ref: G (62.3%) 0.7267612 0.5118811 1.0389096
## 7   7  rs8001641 g (53.2%), ref: A (46.8%) 1.2971752 0.9682742 1.7447377
## 8   8  rs2912771     g (28%), ref: A (72%) 0.7572373 0.5541278 1.0425273
## 9   9  rs1002246 a (32.6%), ref: G (67.4%) 1.2715154 0.9435431 1.7244731
## 10 10  rs6701037 c (44.8%), ref: A (55.2%) 0.7936407 0.5906322 1.0718157
## 11 11  rs7078160 a (20.6%), ref: G (79.4%) 0.8055953 0.6098222 1.0717973
## 12 12   rs766325 g (46.9%), ref: A (53.1%) 1.2512808 0.9250726 1.7142044
## 13 13  rs4621895 t (41.2%), ref: C (58.8%) 1.2311249 0.9074437 1.6950425
## 14 14   rs470563     c (42%), ref: T (58%) 0.8098298 0.5949561 1.1083503
## 15 15  rs7138803 a (33.4%), ref: G (66.6%) 0.8164243 0.5945113 1.1298432
## 16 16   rs987525 a (21.3%), ref: C (78.7%) 0.8441966 0.6472228 1.1093076
## 17 17  rs3752075 c (35.3%), ref: T (64.7%) 1.1956468 0.8946358 1.6094123
## 18 18 rs17782313 c (20.3%), ref: T (79.7%) 0.8437497 0.6427714 1.1211154
## 19 19  rs7864322 c (32.4%), ref: T (67.6%) 0.8237531 0.5945260 1.1518043
## 20 20   rs571312 a (20.4%), ref: C (79.6%) 0.8503870 0.6463622 1.1336630
##      RRR.p.val
## 1  0.002112428
## 2  0.006246328
## 3  0.024213284
## 4  0.046674411
## 5  0.051766208
## 6  0.080862681
## 7  0.081443505
## 8  0.085619288
## 9  0.118744894
## 10 0.126714727
## 11 0.136992528
## 12 0.146070597
## 13 0.182130389
## 14 0.188787688
## 15 0.223087036
## 16 0.225559611
## 17 0.231623488
## 18 0.239445188
## 19 0.254277970
## 20 0.266668447

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

These analyses are for cleft type cntrl!

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:
##      rs29941 rs2235371 rs2912760 rs11084753 rs8001641 rs2912771 rs1002246
## [1,]     456       456       456        456       456       456       456
## [2,]      11        14         3         11         1         1         2
##      rs6701037 rs766325 rs4621895 rs470563 rs7138803 rs987525
## [1,]       456      456       456      456       456      456
## [2,]        20       19         7        8        11        1
  1. for the enhancer region:
##      rs4752028 rs8001641 rs2912771 rs7078160 rs766325 rs470563 rs7138803
## [1,]       456       456       456       456      456      456       456
## [2,]         1         1         1         1        1        1         1
##      rs987525 rs3752075 rs7864322
## [1,]      456       456       456
## [2,]        1         1         1
  1. for the gene region:
##      rs2235371 rs4752028 rs2912760 rs2912771 rs1002246 rs7078160 rs4621895
## [1,]       456       456       456       456       456       456       456
## [2,]         8         3        21        20        28         1         6
##      rs470563 rs3752075
## [1,]      456       456
## [2,]       10        16

Categorizing methylation values

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

## Grouping limits, promoter regions:
##              rs29941   rs2235371   rs2912760 rs11084753   rs8001641
## 0%        -0.8292981 -0.92319540 -0.09432201 -0.8292981 -0.04921919
## 33.33333%  0.1851392  0.07995709  0.93811558  0.1851392  0.97252389
## 66.66667%  0.1888426  0.08121223  0.94738437  0.1888426  0.97689237
## 100%       1.2079032  1.08472736  1.96578368  1.2079032  1.98681766
##             rs2912771    rs1002246  rs6701037    rs766325   rs4621895
## 0%        -0.06395596 -0.994968313 -0.8698007 -0.96761470 -0.97791111
## 33.33333%  0.96227582  0.008675457  0.1520986  0.04107762  0.04751804
## 66.66667%  0.96900564  0.010691215  0.1656524  0.04505021  0.06177037
## 100%       1.98382246  1.017719637  1.2079442  1.05945242  1.10564412
##             rs470563  rs7138803   rs987525
## 0%        -0.1947264 -0.8179770 -0.6064441
## 33.33333%  0.8300076  0.1874735  0.7649811
## 66.66667%  0.8377742  0.1891858  0.8186856
## 100%       1.8520632  1.1971780  1.9279907
## Grouping limits, enhancer regions:
##             rs4752028  rs8001641  rs2912771   rs7078160    rs766325
## 0%        -0.05331135 -0.2760715 -0.2689897 -0.05331135 -0.97800966
## 33.33333%  0.96960934  0.8637778  0.8391328  0.96960934  0.05031837
## 66.66667%  0.97427821  0.8988084  0.8800132  0.97427821  0.06322431
## 100%       1.98548174  1.9626595  1.9533869  1.98548174  1.10677580
##              rs470563  rs7138803    rs987525   rs3752075  rs7864322
## 0%        -0.97728521 -0.2709916 -0.05647725 -0.97728521 -0.1648839
## 33.33333%  0.04971435  0.8323068  0.96794589  0.04971435  0.9191780
## 66.66667%  0.06542580  0.8566212  0.97227496  0.06542580  0.9378857
## 100%       1.13995296  1.9187266  1.98483253  1.13995296  1.9716043
## Grouping limits, gene regions:
##            rs2235371  rs4752028  rs2912760  rs2912771  rs1002246
## 0%        -0.4951531 -0.1937871 -0.2520810 -0.2239480 -0.1449001
## 33.33333%  0.5256034  0.8882802  0.7783994  0.7962287  0.8700875
## 66.66667%  0.5334902  0.9109784  0.7852957  0.8033506  0.8737116
## 100%       1.5570875  1.9465224  1.7994528  1.8183151  1.8848442
##             rs7078160  rs4621895   rs470563  rs3752075
## 0%        -0.05331135 -0.8150516 -0.1737344 -0.1504568
## 33.33333%  0.96960934  0.2137198  0.8601126  0.8771350
## 66.66667%  0.97427821  0.2305664  0.8685060  0.8902507
## 100%       1.98548174  1.2807545  1.8779664  1.9006369

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: 50002, 50004, 50005, 50006, 50008, 50010 ... 51022, 51023, 51026, 51029, 51030, 51031
## INFO: Will select 456 rows and 438 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpWUIZMb/ff5444a437b16.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:  rs29941  is in position:  1 
##   SNP for gene:  rs2235371  is in position:  2 
##   SNP for gene:  rs2912760  is in position:  5 
##   SNP for gene:  rs11084753  is in position:  6 
##   SNP for gene:  rs8001641  is in position:  7 
##   SNP for gene:  rs2912771  is in position:  8 
##   SNP for gene:  rs1002246  is in position:  9 
##   SNP for gene:  rs6701037  is in position:  10 
##   SNP for gene:  rs766325  is in position:  12 
##   SNP for gene:  rs4621895  is in position:  13 
##   SNP for gene:  rs470563  is in position:  14 
##   SNP for gene:  rs7138803  is in position:  15 
##   SNP for gene:  rs987525  is in position:  16
## 
##  HaplinStrat:
## === GENE:  rs29941  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 1 
## INFO: Will select 456 rows and 6 columns.
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac843a25aca.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/RtmpIbWDJ7/ff1ac86a85209f.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac874fc568b.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## Warning: Maximum number of EM iterations reached!
##  Convergence not yet obtained. Setting max.EM.iter higher may help.
## 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:  rs2235371  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 2 
## INFO: Will select 456 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/RtmpIbWDJ7/ff1ac852c0428e.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8728178d6.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 
## 152 152 152 
## 
## 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:  rs2912760  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 5 
## INFO: Will select 456 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/RtmpIbWDJ7/ff1ac8a3f37fe.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac816ae334c.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## Warning: Maximum number of EM iterations reached!
##  Convergence not yet obtained. Setting max.EM.iter higher may help.
## 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:  rs11084753  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 6 
## INFO: Will select 456 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/RtmpIbWDJ7/ff1ac85e343807.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac868e53bc.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 
## 152 152 152 
## 
## 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:  rs8001641  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 7 
## INFO: Will select 456 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/RtmpIbWDJ7/ff1ac86ca2642a.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac872df7ebd.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 
## 152 152 152 
## 
## 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: 8 
## INFO: Will select 456 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/RtmpIbWDJ7/ff1ac860e25ec8.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac860954228.ff
## Warning: Maximum number of EM iterations reached!
##  Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
## 
## Running Haplin on stratum "1"...
## Warning: Maximum number of EM iterations reached!
##  Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...
## Warning: Maximum number of EM iterations reached!
##  Convergence not yet obtained. Setting max.EM.iter higher may help.
## 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 
## 152 152 152 
## 
## Running Haplin on full data file...Done
## 
## Running Haplin on stratum "1"...
## Warning: Maximum number of EM iterations reached!
##  Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
## === GENE:  rs1002246  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 9 
## INFO: Will select 456 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/RtmpIbWDJ7/ff1ac81f71a8.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac84158379c.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 
## 152 152 152 
## 
## 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:  rs6701037  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 10 
## INFO: Will select 456 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/RtmpIbWDJ7/ff1ac85da4475.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac85c0236f9.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 
## 152 152 152 
## 
## 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:  rs766325  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 12 
## INFO: Will select 456 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/RtmpIbWDJ7/ff1ac85067233d.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac852218e5.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 
## 152 152 152 
## 
## 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:  rs4621895  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 13 
## INFO: Will select 456 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/RtmpIbWDJ7/ff1ac85d6e54f3.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8277b94a.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 
## 152 152 152 
## 
## 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:  rs470563  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 14 
## INFO: Will select 456 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/RtmpIbWDJ7/ff1ac8166b1ee.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac81c8569d5.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 
## 152 152 152 
## 
## 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 456 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/RtmpIbWDJ7/ff1ac86d2e2a68.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac854eb4479.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 
## 152 152 152 
## 
## 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:  rs987525  ===
##   1. retrieving the subset of data:
## The output file(s) exist! 
## Provided arguments:
##  --- chosen markers: 16 
## INFO: Will select 456 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/RtmpIbWDJ7/ff1ac8485c2d00.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## opening ff C:/Users/jro049/AppData/Local/Temp/RtmpIbWDJ7/ff1ac8510c4dea.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 
## 152 152 152 
## 
## Running Haplin on full data file...
## Warning: Maximum number of EM iterations reached!
##  Convergence not yet obtained. Setting max.EM.iter higher may help.
## Done
## 
## Running Haplin on stratum "1"...Done
## 
## Running Haplin on stratum "2"...Done
## 
## Running Haplin on stratum "3"...Done
  • plotting results:

## Warning: NAs in confidence intervals

## Warning: NAs in confidence intervals

## Warning: NAs in confidence intervals