compute_pathway_activity {easier} | R Documentation |
Infers pathway activity from counts bulk gene expression using PROGENy method from Holland et al., BBAGRM, 2019 and Schubert et al., Nat Commun, 2018.
compute_pathway_activity( RNA_counts = NULL, remove_sig_genes_immune_response = TRUE, verbose = TRUE )
RNA_counts |
data.frame containing raw counts values with HGNC gene symbols as row names and samples identifiers as column names. |
remove_sig_genes_immune_response |
logical value indicating
whether to remove signature genes involved in the derivation of
hallmarks of immune response. This list is available from easierData
package through |
verbose |
logical value indicating whether to display messages about the number of pathway signature genes found in the gene expression data provided. |
A matrix of activity scores with samples in rows and pathways in columns.
Schubert M, Klinger B, Klunemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Bluthgen N, Saez-Rodriguez J. “Perturbation-response genes reveal signaling footprints in cancer gene expression.” Nature Communications: 10.1038/s41467-017-02391-6
Holland CH, Szalai B, Saez-Rodriguez J. "Transfer of regulatory knowledge from human to mouse for functional genomics analysis." Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 2019. DOI: 10.1016/j.bbagrm.2019.194431.
# 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_counts <- assays(dataset_mariathasan)[["counts"]] # Select a subset of patients to reduce vignette building time. pat_subset <- c( "SAM76a431ba6ce1", "SAMd3bd67996035", "SAMd3601288319e", "SAMba1a34b5a060", "SAM18a4dabbc557" ) RNA_counts <- RNA_counts[, colnames(RNA_counts) %in% pat_subset] # Computation of pathway activity # (Holland et al., BBAGRM, 2019; Schubert et al., Nat Commun, 2018) pathway_activity <- compute_pathway_activity( RNA_counts = RNA_counts, remove_sig_genes_immune_response = TRUE )