diffrep {yamss} | R Documentation |
Performs differential abundance analysis on quantification information
in a CMSslice
object.
diffrep(cms, classes)
cms |
An object of class |
classes |
A character vector of class labels for the samples. |
Differential analysis is performed using the limma
package which
uses empirical Bayes methods in the estimation of feature-wise variances.
A data.frame
containing differential analysis information
including log fold changes and p-values.
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)