compute_Tcell_inflamed: Compute T cell-inflamed signature (Tcell_inflamed) score

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

Compute T cell-inflamed signature (Tcell_inflamed) score

Description

Calculates Tcell_inflamed score using a weighted sum of housekeeping normalized expression of its signature genes, as defined in Cristescu et al., Science, 2018.

Usage

compute_Tcell_inflamed(housekeeping, predictors, weights, RNA_tpm)

Arguments

housekeeping	numeric vector indicating the index of houskeeping genes in RNA_tpm.
predictors	numeric vector indicating the index of predictor genes in RNA_tpm.
weights	numeric vector containing the weights.
RNA_tpm	data.frame containing TPM values with HGNC symbols in rows and samples in columns.

Details

Weights were available at Table S2B from Cristescu R, et al. Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy. Science. (2018) 362:eaar3593. doi: 10.1126/science.aar3593.

Value

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

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 mRNA 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.