retrieveDESeq2Results: Retrieve the results from a DESeq2-analysis using IHW and LFC...

In J0bbie/R2CPCT: Misc. functions to perform import and analysis of WGS and RNA-Seq samples

Description

Retrieve the results from a DESeq2-analysis using IHW and LFC shrinkage.

Usage

retrieveDESeq2Results(DESeq2.Object, contrast, nThreads = 20)

Arguments

DESeq2.Object	(DESeqDataSet): DESeqDataSet of a DESeq2 analysis.
contrast	(character): Contrast of the resulst, e.g.: c('testVariable', 'groupA', 'groupb')
nThreads	(integer): Number of threads using during multi-threading

Value

(tibble) Tibble containing the DESeq2 results.

Author(s)

Job van Riet [e-mail]

See Also

Other RNA-Seq: importArriba(), runArriba()

Examples

DESeq2.allSamples <- DESeq2::DESeqDataSetFromMatrix(countData = countMatrix, colData = samples.meta[match(colnames(countMatrix), samples.meta$sample),], design = ~treatmentType)
DESeq2.allSamples <- DESeq2::DESeq(DESeq2.allSamples, test = 'Wald', parallel = TRUE, BPPARAM = BiocParallel::MulticoreParam(workers = 20))
retrieveDESeq2Results(DESeq2.allSamples)

J0bbie/R2CPCT documentation built on Feb. 24, 2022, 8:15 a.m.