writeReport.DESeq2: Write HTML report for DESeq2 analyses

View source: R/writeReport.DESeq2.r

writeReport.DESeq2R Documentation

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.