compute_Ayers_expIS: Compute Expanded Immune signature (Ayers_expIS) score

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

Compute Expanded Immune signature (Ayers_expIS) score

Description

Calculates Ayers_expIS score as the average expression of its signature genes, as defined in Ayers et al., J. Clin. Invest, 2017.

Usage

compute_Ayers_expIS(matches, RNA_tpm)

Arguments

matches	numeric vector indicating the index of signature genes in RNA_tpm.
RNA_tpm	numeric matrix with rows=genes and columns=samples.

Value

A numeric matrix with rows=samples and columns=Expanded Immune signature score.

References

Ayers, M., Lunceford, J., Nebozhyn, M., Murphy, E., Loboda, A., Kaufman, D.R., Albright, A., Cheng, J.D., Kang, S.P., Shankaran, V., et al. (2017). IFN-y-related mRN A profile predicts clinical response to PD-1 blockade. J. Clin. Invest. 127, 2930–2940. https://doi.org/10.1172/JCI91190.

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