getSigScore: Calculate PD-1hi CD8+ T cell signature score

In Liulab/PD1highCD8Tscore: Quantify PD-1hiCD8+ T cells in tumor environment

Description

You can calculate PD-1hi CD8+ T cell signature score in data mentioned in our paper or your own sequencing data. Or your can calculate your own signature.

Usage

getSigScore(tpm, signature_genes, background = background)

Arguments

tpm	A gene expression matrix contains each gene (in rows) and sample (in columns).
signature_genes	A list of character vectors for gene sets, that can consist of gene IDs.
background	background gene sets for getSigScore, see background for more detail.

Examples

data(Cho)
data(background)
data(PD1hiCD8T_Sig)
getSigScoreRes = getSigScore(Cho$"RNA",list(PD1hiCD8T_Sig$Gene.Name),background = background)

Liulab/PD1highCD8Tscore documentation built on March 15, 2021, 1:14 a.m.