diffrep: Perform differential analysis.

In hansenlab/yamss: Tools for high-throughput metabolomics

Description

Performs differential abundance analysis on quantification information in a CMSslice object.

Usage

diffrep(cms, classes)

Arguments

cms	An object of class CMSslice.
classes	A character vector of class labels for the samples.

Details

Differential analysis is performed using the limma package which uses empirical Bayes methods in the estimation of feature-wise variances.

Value

A data.frame containing differential analysis information including log fold changes and p-values.

Examples

quantmat <- matrix(rnorm(12*5000), nrow = 5000, ncol = 12)
cmsobj <- CMSslice(assays = SimpleList(peakQuants = quantmat))
classes <- rep(c("case", "control"), each = 6)
difftab <- diffrep(cmsobj, classes)

hansenlab/yamss documentation built on Feb. 8, 2022, 4:28 p.m.