Write HTML report from graphs and tables created during the analysis with edgeR
writeReport.edgeR(target, counts, out.edgeR, summaryResults, majSequences,
workDir, projectName, author, targetFile, rawDir, featuresToRemove, varInt,
condRef, batch, alpha, pAdjustMethod, cpmCutoff, colors, gene.selection,
normalizationMethod)target data.frame of the project returned by loadTargetFile()
matrix of counts returned by loadCountData()
the result of run.edgeR()
the result of summarizeResults.DESeq2()
the result of descriptionPlots()
path to the 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
threshold of statistical significance
p-value adjustment method: "BH" (default) or "BY"
counts-per-million cut-off to filter low counts
vector of colors of each biological condition on the plots
selection of the features in MDSPlot() ("pairwise" by default)
normalization method: "TMM" (default), "RLE" (DESeq) or "upperquartile"
This function generates the HTML report for a statistical analysis with edgeR. It uses the tables and graphs created during the workflow as well as the parameters defined at the beginning of the script.