Wrapper to run edgeR: create the dge object, normalize data, estimate dispersions, statistical testing...
run.edgeR(counts, target, varInt, condRef, batch = NULL, cpmCutoff = 1,
normalizationMethod = "TMM", pAdjustMethod = "BH", ...)matrix of counts
target data.frame of the project
name of the factor of interest (biological condition)
reference biological condition
batch effect to take into account (NULL by default)
counts-per-million cut-off to filter low counts
normalization method: "TMM" (default), "RLE" (DESeq) or "upperquartile"
p-value adjustment method: "BH" (default) or "BY"
optional arguments to be passed to glmFit()
A list containing the dge object and the results object