.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.5.
.TH GETPPLR "1" "September 2021" "getPPLR 0.7.5+dfsg" "User Commands"
.SH NAME
getPPLR \- compute PPLR from MCMC expression samples
.SH SYNOPSIS
.B getPPLR
\fI\,-o <outFileName>  \/\fR[\fI\,OPTIONS\/\fR] [\fI\,sampleFile-C1\/\fR] [\fI\,sampleFile-C1\/\fR]
.SH DESCRIPTION
Computes PPLR from MCMC expression samples.
.IP
(the probability of second condition being up\-regulated)
Also computes log2 fold change with confidence intervals, and condition mean log expression.
[sampleFiles] should contain transposed MCMC samples from different conditions.
.SH OPTIONS
.HP
\fB\-\-help\fR
.IP
Show this help information.
.HP
\fB\-d\fR ,   \fB\-\-distribution\fR
.IP
Produce whole distribution of differences. (default: Off)
.HP
\fB\-\-inputIsLogged\fR
.IP
Indicate that the input expression estimates are on log scale. (Not necessary to use with data generated by BitSeq\-0.5.0 and above.) (default: Off)
.HP
\fB\-o\fR <outFileName> ,   \fB\-\-outFile=\fR<outFileName>
.IP
Name of the output file.
.HP
\fB\-s\fR <selectFileName> ,   \fB\-\-selectFile=\fR<selectFileName>
.IP
File containing list of selected transcript IDs (zero based), only these will be reported. Only works with \fB\-\-distribution\fR option.
.HP
\fB\-\-subSample=\fR<subSample>
.IP
Sub\-sample the distributions using a given fraction of expression samples. (default: 1)
.HP
\fB\-v\fR ,   \fB\-\-verbose\fR
.IP
Verbose output. (default: Off)