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

# estimateHyperPar(1)

estimate expression dependent hyperparameters for bitseq

## NAME

estimateHyperPar - estimate expression dependent hyperparameters for bitseq

## SYNOPSIS

**estimateHyperPar** *-o \<outFileName\>*  \[*OPTIONS*\] \[*sampleFiles*\]

## DESCRIPTION

Estimate expression dependent hyperparameters from the dataset.

-

  \[sample Files\] should contain transposed MCMC samples from replicates. To distinguish conditions use C between them e.g.:

-

  samplesC1-R1.rpkm samplesC1-R2.rpkm C samplesC2-R1.rpkm samplesC2-R2.rpkm

## OPTIONS

**--help**

-

  Show this help information.

**--exThreshold=**\<exT\>

-

  Threshold of lowest expression for which the estimation is done. (default: **-5**)

**-g** \<groupsN\> ,   **--groupsNumber=**\<groupsN\>

-

  Number of groups of transcript of similar size. (default: 200)

**-l** \<lambda0\> ,   **--lambda0=**\<lambda0\>

-

  Precision scaling parameter lambda0. (default: 2)

**--lowess-f=**\<lowess-f\>

-

  Parameter F for lowess smoothing specifying amount of smoothing. (default: 0.2)

**--lowess-steps=**\<lowess-steps\>

-

  Parameter Nsteps for lowess smoothing specifying number of iterations. (default: 5)

**--meanFile=**\<meanFileName\>

-

  Name of the file containing joint mean and variance.

**--noforce**

-

  Do not force smoothing of the parameters. (default: Off)

**--norm=**\<normalization\>

-

  Normalization constants for each input file provided as comma separated list of doubles (e.g. 1.0017,1.0,0.9999 ).

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

-

  Name of the output file.

**-p** \<paramsAllFileName\> ,   **--paramsAllFile=**\<paramsAllFileName\>

-

  Name of the file to which to store all parameter values generated prior to lowess smoothing.

**-s** \<samplesN\> ,   **--samplesNumber=**\<samplesN\>

-

  Number of samples generated for each group. (default: 2)

**--seed=**\<seed\>

-

  Random initialization seed.

**-S** ,   **--smoothOnly**

-

  Input file contains previously sampled hyperparameters which should smoothed only. (default: Off)

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

-

  Verbose output. (default: Off)

**-V** ,   **--veryVerbose**

-

  More verbose output. (default: Off)