compute_pathways_scores: Compute pathways score

In olapuentesantana/easier_manuscript: Evaluate patient immune response to ICBs through a systems approach

Description

compute_pathways_scores infers pathway activity from raw counts RNAseq data.

Usage

compute_pathways_scores(RNA.counts, remove.genes.ICB_proxies = TRUE)

Arguments

RNA.counts	numeric matrix of read counts with rows=genes and columns=samples
remove.genes.ICB_proxies	boolean variable to reomove all those genes involved in the computation of ICB proxy's of response

Value

A list with the following elements:

scores

pathway activity matrix with rows=samples and columns=pathwats

transcripts_kept

vector with available gene names

transcripts_left

vector with missing gene names

olapuentesantana/easier_manuscript documentation built on Sept. 22, 2021, 9:42 p.m.