Convert a matrix of raw counts to a matrix of log2(Counts per Million + 1) values

The input can be a base R matrix or a sparse matrix from the Matrix package.

logCPM(counts)

Arguments

counts

a matrix, dgCMatrix, or dgTMatrix of count values.

Value

a matrix, dgCMatrix, or dgTMatrix of log2(CPM + 1) values (matching input)

Details

This function expects that columns correspond to samples, and rows to genes.