writeReport.DESeq2: Write HTML report for DESeq2 analyses

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

Write HTML report for DESeq2 analyses

Description

Write HTML report from graphs and tables created during the analysis with DESeq2

Usage

writeReport.DESeq2(
  target,
  counts,
  out.DESeq2,
  summaryResults,
  majSequences,
  workDir,
  projectName,
  author,
  targetFile,
  rawDir,
  featuresToRemove,
  varInt,
  condRef,
  batch,
  fitType,
  cooksCutoff,
  independentFiltering,
  alpha,
  pAdjustMethod,
  typeTrans,
  locfunc,
  colors
)

Arguments

target	target data.frame of the project returned by loadTargetFile()
counts	matrix of counts returned by loadCountData()
out.DESeq2	the result of run.DESeq2()
summaryResults	the result of summarizeResults.DESeq2()
majSequences	the result of descriptionPlots()
workDir	working directory
projectName	name of the project
author	name of the author of the analysis
targetFile	path to the target file
rawDir	path to the directory containing the counts files
featuresToRemove	vector of features to remove from the counts matrix
varInt	factor of interest (biological condition)
condRef	reference condition for the factor of interest
batch	variable to take as a batch effect
fitType	mean-variance relationship: "parametric" (default) or "local"
cooksCutoff	outliers detection threshold
independentFiltering	TRUE or FALSE to perform the independent filtering or not
alpha	threshold of statistical significance
pAdjustMethod	p-value adjustment method: "BH" or "BY" for instance
typeTrans	transformation for PCA/clustering: "VST" or "rlog"
locfunc	"median" (default) or "shorth" to estimate the size factors
colors	vector of colors of each biological condition on the plots

Details

This function generates the HTML report for a statistical analysis with DESeq2. It uses the tables and graphs created during the workflow as well as the parameters defined at the beginning of the script.

Author(s)

Hugo Varet

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