NAME

       rsem-control-fdr - Filter EBSeq output for statistical significance.

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