# (C) Copyright 2019 Sur Herrera Paredes
#
# This file is part of HMVAR.
#
# HMVAR is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# HMVAR 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. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with HMVAR. If not, see <http://www.gnu.org/licenses/>.
library(HMVAR)
library(tidyverse)
source("functions.r")
args <- list(dir = "hmp.mktest.SPvsTD/",
outdir = "hmp.mktest.SPvsTD.plots",
threshold = 0.01,
outfile = "hmp.mktest.SPvsTD_significant_genes.txt")
if(!dir.exists(args$outdir))
dir.create(args$outdir)
files <- list.files(args$dir)
Res <- NULL
for(f in files){
name <- str_replace(string = f, pattern = "_mktest.txt$", replacement = "")
cat("\t", name, "\n")
mkres <- process_mkres(f, args$dir)
plot_mkres(mkres = mkres, name = name, dir = args$outdir, threshold = args$threshold)
Res <- mkres %>% filter(p.value < args$threshold) %>% mutate(name = name) %>% bind_rows(Res)
}
write_tsv(Res, args$outfile)
# Repeat for the other comparison
args <- list(dir = "qin2012.mktest.DvsND/",
outdir = "qin2012.mktest.DvsND.plots",
threshold = 0.01,
outfile = "qin2012.mktest.DvsND_significant_genes.txt")
if(!dir.exists(args$outdir))
dir.create(args$outdir)
files <- list.files(args$dir)
Res <- NULL
for(f in files){
name <- str_replace(string = f, pattern = "_mktest.txt$", replacement = "")
cat("\t", name, "\n")
mkres <- process_mkres(f, args$dir)
plot_mkres(mkres = mkres, name = name, dir = args$outdir, threshold = args$threshold)
Res <- mkres %>% filter(p.value < args$threshold) %>% mutate(name = name) %>% bind_rows(Res)
}
write_tsv(Res, args$outfile)
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