compute_LR_pairs: Compute ligand-receptor pairs

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

Description

compute_LR_pairs obtain ligand-receptor pairs weights from tpm RNAseq data.

Usage

compute_LR_pairs(
  RNA.tpm,
  remove.genes.ICB_proxies = FALSE,
  compute.cytokines.pairs = FALSE,
  cancertype
)

Arguments

RNA.tpm	numeric matrix of tpm values 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
compute.cytokines.pairs	boolean variable to compute cytokine pairs as well
cancerype	string character

Value

A list with the following elements:

LRpairs

Ligand-leceptor pairs weights matrix in log2(tpm + 1) with rows=samples and columns = L-R pairs

CYTOKINEpairs

Cytokine-Cytokine pairs weights matrix in log2(tpm + 1) with rows=samples and columns = CYTOKINE pairs

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