compute_CCpair_score: Compute cell-cell pair score

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

Compute cell-cell pair score

Description

Derives a score for each cell-cell pair feature.

Usage

compute_CCpair_score(
  celltype1,
  celltype2,
  intercell_network,
  lrpairs_binary,
  lr_frequency,
  compute_log = TRUE
)

Arguments

celltype1	string character with first cell type involved in the interaction.
celltype2	string character with second cell type involved in the interaction.
intercell_network	matrix with data on cell types interaction network. This is available from easierData package through easierData::get_intercell_networks().
lrpairs_binary	binary vector displaying LR pairs with non-zero frequency.
lr_frequency	numeric vector with LR pairs frequency across the whole TCGA database. This is available from easierData package through easierData::get_lr_frequency_TCGA().
compute_log	boolean variable indicating whether the log of the weighted score should be returned.

Value

A numeric vector with weighted scores.

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"
)

# remove ligand receptor pairs that are always NA
na_lrpairs <- apply(lrpair_weights, 2, function(x) {
  all(is.na(x))
})
lrpair_weights <- lrpair_weights[, na_lrpairs == FALSE]

# binarize the data: set a threshold to 10 TPM,
# only pairs where both ligand and receptor have TPM > 10 are kept
lrpairs_binary <- ifelse(lrpair_weights > log2(10 + 1), 1, 0)

# keep only the LR.pairs for which I have (non-zero) frequencies in the TCGA
lr_frequency <- suppressMessages(easierData::get_lr_frequency_TCGA())
lrpairs_binary <- lrpairs_binary[, colnames(lrpairs_binary) %in% names(lr_frequency)]

# cancer type specific network
intercell_networks <- suppressMessages(easierData::get_intercell_networks())
intercell_network_pancan <- intercell_networks[["pancan"]]
celltypes <- unique(c(
  as.character(intercell_network_pancan$cell1),
  as.character(intercell_network_pancan$cell2)
))
celltype1 <- celltypes[1]
celltype2 <- celltypes[1]

# compute the CC score for each patient
CCpair_score <- compute_CCpair_score(celltype1, celltype2,
  intercell_network_pancan,
  lrpairs_binary, lr_frequency,
  compute_log = TRUE
)

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