compute_TF_activity {easier} | R Documentation |
Infers transcription factor (TF) activity from TPM bulk gene expression using DoRothEA method from Garcia-Alonso et al., Genome Res, 2019.
compute_TF_activity(RNA_tpm = NULL, verbose = TRUE)
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. |
A numeric matrix of activity scores with samples in rows and TFs in columns.
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.
# 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 )