sleuthWrapper: Runs a spike-in differential expression analysis using...

In plger/RNAontheBENCH: RNAontheBENCH - Benchmark of RNAseq quantification and DEA

Description

Runs a differential expression analysis using sleuth and compares it to real differences between spike-in mixes. Currently only for the 12-samples dataset.

Usage

sleuthWrapper(name, folders = NULL, norm = "TMM", savePlot = FALSE)

Arguments

name	A string indicating the name of the analysis/pipeline form which the quantification comes. Will be used in filenames, plot titles, etc.
norm	The normalization method to use (either "linear", or any of the methods supported by edgeR's calcNormFactors. Defaults to 'TMM'.
savePlot	Logical, whether to save the plot in the current working directory (default TRUE).
folder	A character vector containing the path to the Salmon/Sailfish/Kallisto quantification folders. If missing, will look for names matching "AJ" in the current working directory.

Value

A data.frame with the results of the differential expression analysis, as well as a plot.

plger/RNAontheBENCH documentation built on May 25, 2019, 8:22 a.m.