scaleCounts: Scaling raw counts from each sample.

In GfellerLab/EPIC: Estimate the Proportion of Immune and Cancer cells

Scaling raw counts from each sample.

Description

Normalizing the sum of counts from each sample to 1e6.

Usage

scaleCounts(counts, sigGenes = NULL, renormGenes = NULL, normFact = NULL)

Details

Function taking a matrix (genes x samples) of counts as input and returning the scaled counts for the subset signature genes (or all genes if it sigGenes is NULL), with the scaled counts computed based on all the 'renormGenes' (or all genes if it is NULL). The renormalization is made independently for each sample, to have the sum of each columns over the renormGenes equal to 1e6.

normFact, if not null, is used as the normalization factor instead of the colSums (used to renormalize the refProfiles.var by the same amount than the refProfiles).

GfellerLab/EPIC documentation built on July 22, 2023, 2:06 a.m.