compute_IMPRES_MSI: Compute Immuno-Predictive Score (IMPRES) and Micro Satellite...

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

Compute Immuno-Predictive Score (IMPRES) and Micro Satellite Instability (MSI) status score

Description

Calculates IMPRES score by logical comparison of checkpoint gene pairs expression, as defined in Auslander et al., Nat. Med., 2018.

Usage

compute_IMPRES_MSI(sig, len, match_F_1, match_F_2, RNA_tpm)

Arguments

sig	can be either 'IMPRES' or 'MSI'.
len	the length of gene_1 vector.
match_F_1	numeric vector indicating the index of signature genes defined in 'gene_1' in RNA_tpm.
match_F_2	numeric vector indicating the index of signature genes defined in 'gene_2' in RNA_tpm.
RNA_tpm	data.frame containing TPM values with HGNC symbols in rows and samples in columns.

Details

Calculates MSI status score by logical comparison of MSI-related gene pairs, as defined in Fu et al., BMC Genomics, 2019.

Value

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

References

Auslander,N., Zhang,G., Lee,J.S., Frederick, D.T., Miao, B., Moll,T.,Tian, T., Wei,Z., Madan, S., Sullivan, R.J., et al. (2018). Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma. Nat. Med. 24, 1545–1549. https://doi.org/10.1038/s41591-018-0157-9.

Fu, Y., Qi, L., Guo, W., Jin, L., Song, K., You, T., Zhang, S., Gu, Y., Zhao, W., and Guo, Z. (2019). A qualitative transcriptional signature for predicting microsatellite instability status of right-sided Colon Cancer. BMC Genomics 20, 769.

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