Scripts for "No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution"
Scripts necessary to reproduce Figures 1C&D, 2, 6 and 7 as well as Tables 1 and S3 were contributed by Anne-Ruxandra Carvunis These are R scripts that take as input the files "GeneData6.txt" and "dm3_mixed_map.txt". Please modify the address for these files according to where you download them in the #DATA section of the scripts.
was used to calculate log-odds and p-values for Figures 3, 4 and 5. Results of these analyses can be found in Table S2.
# take input file, calculate hypergeometric test and write it all to output file
./calculate_hyper.R -i ./t/data/Figure3/ectoderm.txt -o ./t/data/Figure3/ectoderm_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.
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.
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.