Convert a matrix of raw counts to a matrix of Counts per Million values

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

Usage

cpm(counts, sf = NULL, denom = 1e+06, cells.as.rows = FALSE)

counts: a matrix, dgCMatrix, or dgTMatrix of count values.
sf: vector of numeric values representing the total number of reads. If count matrix includes all genes, value calulated by default (sf=NULL) will be accurate; however, if count matrix represents only a small fraction of genes, we recommend also providing this value.
denom: Denominator that all counts will be scaled to. The default (1 million) is commonly used, but 10000 is also common for sparser droplet-based sequencing methods.
cells.as.rows: Set to FALSE (default) if rows are genes and columns are cells or TRUE if rows are cells and columns are genes.

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

This function expects that columns correspond to samples, and rows to genes, but can also take the transpose if specified by cells.as.rows=TRUE.