fit: Fit the negative binomial distribution

In gagneurlab/OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

Fit the negative binomial distribution

Description

Fit a negative binomial (NB) distribution to the counts per gene over all samples using, if available, the precomputed control factors. If no normalization factors are provided only the sizeFactors are used.

Usage

## S3 method for class 'OutriderDataSet'
fit(object, BPPARAM = bpparam(), ...)

Arguments

object	An OutriderDataSet
BPPARAM	by default bpparam()
...	Currently not used.

Value

An OutriderDataSet object with the fitted model. Accessible through: mcols(ods)[,c('mu', 'theta')].

Examples

ods <- makeExampleOutriderDataSet()
ods <- estimateSizeFactors(ods)
ods <- fit(ods)

mcols(ods)[1:10,c('mu', 'theta')]

gagneurlab/OUTRIDER documentation built on April 29, 2024, 2:22 a.m.