.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.11.
.TH ESTIMATEDE "1" "September 2019" "estimateDE 0.7.5+dfsg" "User Commands"
.SH NAME
estimateDE \- this bitseq module estimates differential expression from data sets
.SH SYNOPSIS
.B estimateDE
\fI\,-o <outFilePrefix> -p <parFileName>  \/\fR[\fI\,OPTIONS\/\fR] [\fI\,sampleFiles\/\fR]
.SH DESCRIPTION
Estimate differential expression from the dataset.
.IP
[sampleFiles] should contain transposed MCMC samples from replicates.
To distinguish conditions use C between them e.g.:
.IP
samplesC1\-R1.rpkm samplesC1\-R2.rpkm C samplesC2\-R1.rpkm samplesC2\-R2.rpkm
.SH OPTIONS
.HP
\fB\-\-help\fR
.IP
Show this help information.
.HP
\fB\-\-confidenceInterval=\fR<cf>
.IP
Percentage for confidence intervals. (default: 95)
.HP
\fB\-l\fR <lambda0> ,   \fB\-\-lambda0=\fR<lambda0>
.IP
Parameter lambda_0. (default: 2)
.HP
\fB\-\-norm=\fR<normalization>
.IP
Normalization constants for each input file provided as comma separated list of doubles (e.g. 1.0017,1.0,0.9999 ).
.HP
\fB\-o\fR <outFilePrefix> ,   \fB\-\-outPrefix=\fR<outFilePrefix>
.IP
Prefix for the output files.
.HP
\fB\-p\fR <parFileName> ,   \fB\-\-parameters=\fR<parFileName>
.IP
File containing estimated hyperparameters.
.HP
\fB\-s\fR ,   \fB\-\-samples\fR
.IP
Produce samples of condition mean expression apart from PPLR and confidence. (default: Off)
.HP
\fB\-\-seed=\fR<seed>
.IP
Random initialization seed.
.HP
\fB\-v\fR ,   \fB\-\-verbose\fR
.IP
Verbose output. (default: Off)