compute_RIR: Compute three scores from the immune resistance program:...

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

Compute three scores from the immune resistance program: resF_down (RIR), resF_up, resF (resF_up - resF_down)

Description

Calculates RIR score by combining a set of gene signatures associated with upregulation and downregulation of T cell exclusion, post-treatment and functional resistance. We used the original approach defined in Jerby-Arnon et al., Cell, 2018.

Usage

compute_RIR(RNA_tpm, RIR_program)

Arguments

RNA_tpm	data.frame containing TPM values with HGNC symbols in rows and samples in columns.
RIR_program	list with gene signatures included in the immune resistance program from Jerby-Arnon et al., 2018.

Details

The gene signatures were provided by original work: https://github.com/livnatje/ImmuneResistance

Value

A numeric matrix with samples in rows and three RIR scores as columns: "resF_up" (upregulated score), "resF_down" (downregulated score) and "resF" (upregulated score - downregulated score).

References

Jerby-Arnon, L., Shah, P., Cuoco, M.S., Rodman, C., Su, M.-J., Melms, J.C., Leeson, R., Kanodia, A., Mei, S., Lin, J.-R., et al. (2018). A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell 175, 984–997.e24. https://doi.org/10.1016/j.cell.2018.09.006.

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