compute_TF_activity: Compute transcription factor activity from gene expression...

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

Compute transcription factor activity from gene expression using DoRothEA

Description

Infers transcription factor (TF) activity from TPM bulk gene expression using DoRothEA method from Garcia-Alonso et al., Genome Res, 2019.

Usage

compute_TF_activity(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 regulated genes found in the gene expression data provided.

Value

A numeric matrix of activity scores with samples in rows and TFs in columns.

References

Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J. "Benchmark and integration of resources for the estimation of human transcription factor activities." Genome Research. 2019. DOI: 10.1101/gr.240663.118.

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 TF activity (Garcia-Alonso et al., Genome Res, 2019)
tf_activity <- compute_TF_activity(
  RNA_tpm = RNA_tpm
)

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