compute_CC_pairs {easier} | R Documentation |
Infers scores of cell-cell interactions in the tumor
microenvironment (Lapuente-Santana et al., Patterns, 2021) using
the ligand-receptor weights obtained from compute_LR_pairs
as input.
compute_CC_pairs(lrpairs = NULL, cancer_type = "pancan", verbose = TRUE)
lrpairs |
output of the compute_LR_pairs function. A matrix
of log2(TPM +1) weights with samples in rows and ligand-receptor
pairs in columns. This is the output from |
cancer_type |
string detailing the cancer type whose cell-cell interaction network will be used. By default, a pan-cancer network is selected 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 |
logical value indicating whether to display informative messages about the process. |
A matrix of scores with samples in rows and cell-cell 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.
# 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" ) # Computation of cell-cell interaction scores ccpair_scores <- compute_CC_pairs( lrpairs = lrpair_weights, cancer_type = "pancan" )