brcasurv

Helper functions to estimate the survival associations of user-provided gene signatures in TCGA & METABRIC.

Installation:

devtools::install_github("montilab/brcasurv")

Example Usage:

Given a named list of gene sets e.g. list(GS1 = c("gene1", "gene2", "gene3")) one can score each sample in TCGA/METABRIC with gsva_data and use gsva_cox_fit to fit coxph models.

gsva_data <- gsva_data(sigs_list = sigs_list, 
                       brca_data = "TCGA", # Or "METABRIC"
                       adjust_prolif = TRUE, 
                       adjust_inflam = TRUE)

gsva_cox_fits <- gsva_cox_fit(gsva_data, 
                              adjust_age = TRUE,
                              adjust_prolif = TRUE,
                              adjust_inflam = TRUE)