run.DESeq2_corset: Wrapper to run DESeq2

Description Usage Arguments Value Author(s)

View source: R/run.DESeq2_corset.r

Description

Wrapper to run DESeq2: create the DESeqDataSet, normalize data, estimate dispersions, statistical testing...

Usage

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run.DESeq2_corset(counts, target, varInt, batch = NULL,
  locfunc = "median", fitType = "parametric", pAdjustMethod = "BH",
  alpha = 0.05, ...)

Arguments

counts

matrix of raw counts

target

target data.frame of the project

varInt

name of the factor of interest (biological condition)

batch

batch effect to take into account (NULL by default)

locfunc

"median" (default) or "shorth" to estimate the size factors

fitType

mean-variance relationship: "parametric" (default) or "local"

pAdjustMethod

p-value adjustment method: "BH" (default) or "BY" for instance

alpha

significance threshold to apply to the adjusted p-values

...

optional arguments to be passed to nbinomWaldTest()

independentFiltering

TRUE or FALSE to perform the independent filtering or not

Value

A list containing the dds object (DESeqDataSet class), the results objects (DESeqResults class) and the vector of size factors

Author(s)

Aditya Narayan Sarangi


sarangian/deaRscripts documentation built on Dec. 12, 2019, 12:48 a.m.