compute_LR_pairs {easier} | R Documentation |
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.
compute_LR_pairs(RNA_tpm = NULL, cancer_type = "pancan", verbose = TRUE)
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. |
A matrix of weights with samples in rows and ligand-receptor pairs in columns.
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
# 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]