---
name: "getPPLR"
section: "1"
platform: "linux"
package: "bitseq"
version: "0.7.5+dfsg-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/getPPLR"
---

# getPPLR(1)

compute PPLR from MCMC expression samples

## NAME

getPPLR - compute PPLR from MCMC expression samples

## SYNOPSIS

**getPPLR** *-o \<outFileName\>*  \[*OPTIONS*\] \[*sampleFile-C1*\] \[*sampleFile-C1*\]

## DESCRIPTION

Computes PPLR from MCMC expression samples.

-

  (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.

## OPTIONS

**--help**

-

  Show this help information.

**-d** ,   **--distribution**

-

  Produce whole distribution of differences. (default: Off)

**--inputIsLogged**

-

  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)

**-o** \<outFileName\> ,   **--outFile=**\<outFileName\>

-

  Name of the output file.

**-s** \<selectFileName\> ,   **--selectFile=**\<selectFileName\>

-

  File containing list of selected transcript IDs (zero based), only these will be reported. Only works with **--distribution** option.

**--subSample=**\<subSample\>

-

  Sub-sample the distributions using a given fraction of expression samples. (default: 1)

**-v** ,   **--verbose**

-

  Verbose output. (default: Off)