Calculating p-values

[mdozmorov]

We need to calculate p-values using Fisher's exact test only, using strategu in https://github.com/mdozmorov/R.genomerunner/blob/master/genomeRunner_file_formatting_functions2.R

Data for testing:

infile <- "/Users/mikhail/Documents/Work/GenomeRunner/Paper-Similarity/data_Farh/ENCODE_Dgf/detailed.txt" cases when OR equal to 0 foi_obs n_fois bkg_obs n_bkg 1 0 155 203 7735 2 0 46 938 7735 3 0 47 938 7735 4 0 195 189 7735 5 0 175 161 7735 6 0 46 816 7735 7 0 195 177 7735 8 0 197 151 7735 9 0 234 176 7735 10 0 43 712 7735 11 0 195 200 7735 12 0 195 224 7735 13 0 173 187 7735 14 0 46 754 7735 15 0 46 776 7735 16 0 47 752 7735 17 0 141 218 7735 18 0 46 773 7735 19 0 195 180 7735 20 0 46 652 7735 21 0 234 194 7735 22 0 175 194 7735 23 0 195 179 7735

"/Users/mikhail/Documents/Work//GenomeRunner/gwas2bed/autoimmune/R.GR.autoimmune/data.gr/Roadmap_chromStates18/detailed.txt" cases when OR equal to infinity. With "" also have significant p-value, thus not overlap 1. foi_obs n_fois bkg_obs n_bkg 1 1 696 1 7735 2 1 261 1 7735 3 1 63 1 7735 4 1 110 1 7735 5 1 696 1 7735 6 1 370 1 7735 7 1 264 1 7735 8 2 696 2 7735 9 1 430 1 7735 10 1 696 1 7735 11 1 175 1 7735 12 2 787 2 7735 13 1 339 1 7735 14 2 696 2 7735 15 46 46 3850 7735 16 1 696 1 7735 17 46 46 4717 7735 18 46 46 4109 7735 19 2 787 2 7735 20 1 192 1 7735 21 46 46 4165 7735 22 1 787 1 7735 23 1 175 1 7735

[lkscara]

Fixed in b8c6c622187c6eac0acd4509de1f41f3f035a4b6