run.DESeq2_trans: Wrapper to run DESeq2

Description Usage Arguments Value Author(s)

View source: R/run.DESeq2_Salmon.r View source: R/run.DESeq2_Salmon.r View source: R/run.DESeq2_trans.r

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

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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.