RSEM-CONTROL-FDR(1)

NAME
rsem-control-fdr

SYNOPSIS
rsem-control-fdr [options] input_file fdr_rate output_file

ARGUMENTS

input_file
    This should be the main result file generated by 'rsem-run-ebseq', which contains all genes/transcripts and their associated statistics.

fdr_rate
    The desire false discovery rate (FDR).

output_file
    This file is a subset of the 'input_file'. It only contains the genes/transcripts called as differentially expressed (DE). When more than 2 conditions exist, DE is defined as not all conditions are equally expressed. Because statistical significance does not necessarily mean biological significance, users should also refer to the fold changes to decide which genes/transcripts are biologically significant. When more than two conditions exist, this file will not contain fold change information and users need to calculate it from 'input_file.condmeans' by themselves.

OPTIONS

--hard-threshold
    Use hard threshold method to control FDR. If this option is set, only those genes/transcripts with their PPDE >= 1 - fdr_rate are called as DE. (Default: on)

--soft-threshold
    Use soft threshold method to control FDR. If this option is set, this program will try to report as many genes/transcripts as possible, as long as their average PPDE >= 1 - fdr_rate. This option is equivalent to use EBSeq's 'crit_fun' for FDR control. (Default: off)

-h/--help
    Show help information.

DESCRIPTION
This program controls the false discovery rate and reports differentially expressed genes/transcripts.

EXAMPLES
We assume that we have 'GeneMat.results' as input. We want to control FDR at 0.05 using hard threshold method and name the output file as 'GeneMat.de.txt':

 rsem-control-fdr GeneMat.results 0.05 GeneMat.de.txt