calculate_hyper.R - R script to calculate log-odds, hypergeometric test, FDR and Bonferroni correction.
# take input file,calculate hypergeometric test and write it all to output file
./calculate_hyper.R -i ./t/data/disease.txt -o ./t/data/disease_hyper.txt
This script requires input file in TabSeparated format with this header:
phylostrata\tphylostrata_name\tFunctional term\tquant\tsample\thit\ttotal
after header paste your values like this:
1\tCellular organisms\tdisease_genes\t970\t8285\t1760\t22845
it will then calculate log-odds, hypergeometric test, FDR and Bonferroni correction and write it to tsv file.
No configuration.
Copyright (C) <2016> <Martin Sebastijan Šestak> (sestakm@yahoo.com). All rights reserved.
Copyright (C) Martin Sebastijan Šestak (sestakm@yahoo.com)
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See L.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.