fit: Fit the negative binomial distribution

Description Usage Arguments Value Examples

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

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## 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

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

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

gagneurlab/OUTRIDER documentation built on Oct. 24, 2020, 6:49 p.m.