checkParameters.DESeq2: Check the parameters (when using DESeq2)

In PF2-pasteur-fr/SARTools: Statistical Analysis of RNA-Seq Tools

Check the parameters (when using DESeq2)

Description

Check the format and the validity of the parameters which will be used for the analysis with DESeq2.

Usage

checkParameters.DESeq2(
  projectName,
  author,
  targetFile,
  rawDir,
  featuresToRemove,
  varInt,
  condRef,
  batch,
  fitType,
  cooksCutoff,
  independentFiltering,
  alpha,
  pAdjustMethod,
  typeTrans,
  locfunc,
  colors
)

Arguments

projectName	name of the project
author	author of the statistical analysis/report
targetFile	path to the design/target file
rawDir	path to the directory containing raw counts files
featuresToRemove	names of the features to be removed
varInt	factor of interest
condRef	reference biological condition
batch	blocking factor in the design
fitType	mean-variance relationship: "parametric" (default) or "local"
cooksCutoff	outliers detection (TRUE or FALSE)
independentFiltering	TRUE/FALSE to perform independent filtering
alpha	threshold of statistical significance
pAdjustMethod	p-value adjustment method: "BH" (default) or "BY" for example
typeTrans	transformation for PCA/clustering: "VST" ou "rlog"
locfunc	"median" (default) or "shorth" to estimate the size factors
colors	vector of colors of each biological condition on the plots

Value

A boolean indicating if there is a problem in the parameters

Author(s)

Hugo Varet

PF2-pasteur-fr/SARTools documentation built on April 6, 2022, 2:24 a.m.