Write HTML report from graphs and tables created during the analysis with DESeq2
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)target data.frame of the project returned by loadTargetFile()
matrix of counts returned by loadCountData()
the result of run.DESeq2()
the result of summarizeResults.DESeq2()
the result of descriptionPlots()
working directory
name of the project
name of the author of the analysis
path to the target file
path to the directory containing the counts files
vector of features to remove from the counts matrix
factor of interest (biological condition)
reference condition for the factor of interest
variable to take as a batch effect
mean-variance relationship: "parametric" (default) or "local"
outliers detection threshold
TRUE or FALSE to perform the independent filtering or not
threshold of statistical significance
p-value adjustment method: "BH" or "BY" for instance
transformation for PCA/clustering: "VST" or "rlog"
"median" (default) or "shorth" to estimate the size factors
vector of colors of each biological condition on the plots
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.