NBAMSeq: Differential expression analysis based on negative binomial...

Description Usage Arguments Value References Examples

View source: R/NBAMSeq.R

Description

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

Usage

1
2
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

1
2
gsd = makeExample(n = 3, m = 10)
gsd = NBAMSeq(gsd)

reese3928/NBAMSeq documentation built on Oct. 29, 2020, 8:06 a.m.