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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 MAX_FDR MIN_FC\n\n"
. " \n\tRun this in the edgeR results directory.\n\n";
my $MAX_FDR = $ARGV[0] or die $usage;
my $MIN_FC = $ARGV[1] or die $usage;
my $MIN_LOGFC = log($MIN_FC)/log(2);
main: {
my @DE_files = <*.DE_results>;
my %sample_to_comparison_count;
my %sample_to_DE_genes;
foreach my $DE_file (@DE_files) {
$DE_file =~ /\.([^\.]+)_vs_([^\.]+)/ or die "Error, cannot extract sample names from filename: $DE_file";
my $sample_A = $1;
my $sample_B = $2;
$sample_to_comparison_count{$sample_A}++;
$sample_to_comparison_count{$sample_B}++;
open (my $fh, $DE_file) or die "Error, cannot open file $DE_file";
my $header = <$fh>;
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $logFC = $x[1];
my $FDR = $x[4];
unless ($FDR <= $MAX_FDR && abs($logFC) >= $MIN_LOGFC) { next; }
my $gene = $x[0];
if ($logFC < 0) {
$sample_to_DE_genes{$sample_A}->{$gene}++;
}
else {
$sample_to_DE_genes{$sample_B}->{$gene}++;
}
}
close $fh;
}
foreach my $sample (keys %sample_to_DE_genes) {
foreach my $gene (keys %{$sample_to_DE_genes{$sample}}) {
my $count_DE_induced = $sample_to_DE_genes{$sample}->{$gene};
my $num_sample_comparisons = $sample_to_comparison_count{$sample};
if ($count_DE_induced == $num_sample_comparisons) {
## DE and induced in each comparison
print "$gene\t$sample\n";
}
}
}
exit(0);
}
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