Fisher's exact test wrapper Codes to perform one-tailed fisher's exact test. The alternative hypothesis is OR>1. In which OR = (In_Both * In_Neither)/(In_markerlist_only * Identified_only). Example to run the code (from command line):
Rscript FET.R Allgenes.txt geneList.txt geneIdentified.txt FET_out.txt
The inputs for the code are:
- [FileNameIn1] Input file contains names of all genes. Each gene in one row
- [FileNameIn2] Input file contains names of the marker list of interest. Each gene in one row
- [FileNameIn3] Input file contains names of the identified genes. Each gene in one row
- [FileNameOut] Output file name. The output file contains two numbers - fisher's exact test p value and log p value.
The contigency table, test statatistics and confidence intervals will be shown in console.
Note genes in file2 or 3 but not in file 1 will be excluded prior to analysis.