NBAMSeq {NBAMSeq}R Documentation

Differential expression analysis based on negative binomial additive model

Description

This function performs differential expression analysis based on negative binomial additive model.

Usage

NBAMSeq(object, gamma = 2.5, parallel = FALSE, fitlin = FALSE,
  BPPARAM = bpparam(), ...)

Arguments

object

a NBAMSeqDataSet object

gamma

a number greater or equal to 1. Increase gamma to create smoother models. Default gamma is 2.5. See gam for details.

parallel

either TRUE or FALSE indicating whether parallel should be used. Default is FALSE

fitlin

either TRUE or FALSE indicating whether linear model should be fitted. Default is FALSE

BPPARAM

an argument provided to bplapply. See register for details.

...

additional arguments provided to gam

Value

a NBAMSeqDataSet object

References

Love, M.I., Huber, W., Anders, S. (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15:550. https://doi.org/10.1186/s13059-014-0550-8

Examples

gsd = makeExample(n = 3, m = 10)
gsd = NBAMSeq(gsd)

[Package NBAMSeq version 1.8.0 Index]