compute_CC_pairs: Compute cell-cell interactions scores using computed...

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

Compute cell-cell interactions scores using computed ligand-receptor weights

Description

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.

Usage

compute_CC_pairs(lrpairs = NULL, cancer_type = "pancan", verbose = TRUE)

Arguments

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 compute_LR_pairs.
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.

Value

A matrix of scores with samples in rows and cell-cell 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.

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"
)

# Computation of cell-cell interaction scores
ccpair_scores <- compute_CC_pairs(
  lrpairs = lrpair_weights,
  cancer_type = "pancan"
)

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