compute_LR_pairs: Compute ligand-receptor pair weights from TPM bulk gene...

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

Compute ligand-receptor pair weights from TPM bulk gene expression

Description

Quantifies ligand-receptor interactions in the tumor microenvironment from TPM bulk gene expression (Lapuente-Santana et al., Patterns, 2021) by using prior knowledge coming from ligand-receptor pair annotations from the database of Ramilowski (Ramilowski et al., Nat Commun, 2015). Each ligand-receptor weight is defined as the minimum of the log2(TPM+1) expression of the ligand and the receptor.

Usage

compute_LR_pairs(RNA_tpm = NULL, cancer_type = "pancan", verbose = TRUE)

Arguments

RNA_tpm	A data.frame containing TPM values with HGNC symbols in rows and samples in columns.
cancer_type	A string detailing the cancer type whose ligand-receptor pairs network will be used. A pan-cancer network is selected by default, whose network represents the union of all ligand-receptor pairs present across the 18 cancer types studied in Lapuente-Santana et al., Patterns, 2021.
verbose	A logical value indicating whether to display messages about the number of ligand-receptor genes found in the gene expression data provided.

Value

A matrix of weights with samples in rows and ligand-receptor pairs in columns.

References

Oscar Lapuente-Santana, Maisa van Genderen, Peter A. J. Hilbers, Francesca Finotello, and Federica Eduati. 2021. Interpretable Systems Biomarkers Predict Response to Immune-Checkpoint Inhibitors. Patterns, 100293. https://doi.org/10.1016/j.patter.2021.100293.

Ramilowski, J., Goldberg, T., Harshbarger, J. et al. A draft network of ligand–receptor-mediated multicellular signalling in human. Nat Commun 6, 7866 (2015). https://doi.org/10.1038/ncomms8866

Examples

# using a SummarizedExperiment object
library(SummarizedExperiment)
# Using example exemplary dataset (Mariathasan et al., Nature, 2018)
# from easierData. Original processed data is available from
# IMvigor210CoreBiologies package.
library("easierData")

dataset_mariathasan <- easierData::get_Mariathasan2018_PDL1_treatment()
RNA_tpm <- assays(dataset_mariathasan)[["tpm"]]

# Select a subset of patients to reduce vignette building time.
pat_subset <- c(
  "SAM76a431ba6ce1", "SAMd3bd67996035", "SAMd3601288319e",
  "SAMba1a34b5a060", "SAM18a4dabbc557"
)
RNA_tpm <- RNA_tpm[, colnames(RNA_tpm) %in% pat_subset]

# Computation of ligand-receptor pair weights
lrpair_weights <- compute_LR_pairs(
  RNA_tpm = RNA_tpm,
  cancer_type = "pancan"
)
lrpair_weights[1:5, 1:5]

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