compute_chemokines: Compute chemokine signature (chemokines) score

In olapuentesantana/easier: Estimate Systems Immune Response from RNA-seq data

Compute chemokine signature (chemokines) score

Description

Calculates chemokines score as the PC1 score that results from applying PCA to the expression of its signature genes, defined in Messina et al., Sci. Rep., 2012.

Usage

compute_chemokines(matches, RNA_tpm)

Arguments

matches	numeric vector indicating the index of signature genes in RNA_tpm.
RNA_tpm	data.frame containing TPM values with HGNC symbols in rows and samples in columns.

Value

A numeric matrix with samples in rows and chemokines score in a column.

References

Messina, J.L., Fenstermacher, D.A., Eschrich, S., Qu, X., Berglund, A.E., Lloyd, M.C., Schell, M.J., Sondak, V.K., Weber, J.S., and Mule, J.J. (2012). 12-Chemokine gene signature identifies lymph node-like structures in melanoma: potential for patient selection for immunotherapy? Sci. Rep. 2, 765. https://doi.org/10.1038/srep00765.

olapuentesantana/easier documentation built on Feb. 25, 2024, 3:39 p.m.