results: Pulling out result

Description Usage Arguments Value References Examples

View source: R/results.R

Description

This function pulls out result from NBAMSeqDataSet object returned by NBAMSeq

Usage

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results(object, name, contrast, indepfilter = TRUE, alpha = 0.1,
  pAdjustMethod = "BH", parallel = FALSE, BPPARAM = bpparam(), ...)

Arguments

object

a NBAMSeqDataSet object returned by NBAMSeq

name

the name of nonlinear variable or continuous linear variable

contrast

a character of length 3. 1st element: name of factor variable; 2nd element: name of numerator level; 3rd element: name of denominator level. contrast = c("group", "treatment", "control") means comparing treatment vs control for group variable.

indepfilter

either TRUE or FALSE indicating whether independent filtering should be performed. Default is TRUE.

alpha

significant threhold for declaring genes as differentially expressed. Default is 0.1.

pAdjustMethod

pvalue adjustment method. Default is "BH". See p.adjust for details.

parallel

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

BPPARAM

an argument provided to bplapply. See register for details.

...

additional arguments provided to pvalueAdjustment function in DESeq2. See results for details.

Value

a DataFrame which contains the result

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

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gsd = makeExample(n = 3, m = 10)
gsd = NBAMSeq(gsd)
res = results(gsd, name = "pheno")

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