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

In NBAMSeq: Negative Binomial Additive Model for RNA-Seq Data

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)

NBAMSeq documentation built on Nov. 8, 2020, 6:26 p.m.