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R script that will calculate log-odds, hypergeometric test, FDR and Bonferroni correction

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msestak/calculate_hypergeometric_test

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NAME

calculate_hyper.R - R script to calculate log-odds, hypergeometric test, FDR and Bonferroni correction.

SYNOPSIS

# 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

DESCRIPTION

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.

CONFIGURATION

No configuration.

AUTHOR

Copyright (C) <2016> <Martin Sebastijan Šestak> (sestakm@yahoo.com). All rights reserved.

LICENSE

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.

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R script that will calculate log-odds, hypergeometric test, FDR and Bonferroni correction

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