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