run.DESeq2_trans: Wrapper to run DESeq2

In sarangian/RNASeqDEA: Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups

Description

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

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

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

Usage

run.DESeq2_trans(counts, target, varInt, batch = NULL,
  locfunc = "median", fitType = "parametric", pAdjustMethod = "BH",
  alpha = 0.05, ...)

run.DESeq2_trans(counts, target, varInt, batch = NULL,
  locfunc = "median", fitType = "parametric", pAdjustMethod = "BH",
  alpha = 0.05, ...)

run.DESeq2_trans(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
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
independentFiltering	TRUE or FALSE to perform the independent filtering or not
alpha	significance threshold to apply to the adjusted p-values
...	optional arguments to be passed to nbinomWaldTest()
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
independentFiltering	TRUE or FALSE to perform the independent filtering or not
alpha	significance threshold to apply to the adjusted p-values
...	optional arguments to be passed to nbinomWaldTest()

Value

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

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

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

Author(s)

Aditya Narayan Sarangi

Aditya Narayan Sarangi

Aditya Narayan Sarangi

sarangian/RNASeqDEA documentation built on Dec. 8, 2019, 5:24 p.m.