compute_cell_fractions {easier}R Documentation

Compute immune cell fractions from gene expression using quanTIseq

Description

Estimates cell fractions from TPM bulk gene expression using quanTIseq method from Finotello et al., Genome Med, 2019.

Usage

compute_cell_fractions(RNA_tpm = NULL, verbose = TRUE)

Arguments

RNA_tpm

data.frame containing TPM values with HGNC symbols in rows and samples in columns.

verbose

logical value indicating whether to display messages about the number of immune cell signature genes found in the gene expression data provided.

Value

A numeric matrix of normalized enrichment scores with samples in rows and cell types in columns.

References

Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H, Krogsdam A, Loncova Z, Posch W, Wilflingseder D, Sopper S, Ijsselsteijn M, Brouwer TP, Johnson D, Xu Y, Wang Y, Sanders ME, Estrada MV, Ericsson-Gonzalez P, Charoentong P, Balko J, de Miranda NFDCC, Trajanoski Z. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Medicine, 2019. 11(1):34. https://doi.org/10.1186/s13073-019-0638-6

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 cell fractions (Finotello et al., Genome Med, 2019)
cell_fractions <- compute_cell_fractions(RNA_tpm = RNA_tpm)

[Package easier version 0.99.12 Index]