list_cosmic {seqCAT} | R Documentation |
List all available samples in the COSMIC database
list_cosmic(file_path)
file_path |
The file containing COSMIC data (path). |
This function lists the available sample names in the provided COSMIC file (e.g. CosmicCLP_MutantExport.tsv.gz), and takes about half the time it takes to read the full file with the read_cosmic function, making it useful for just seeing if your particular sample is listed in COSMIC or not.
A vector of sample names
file <- system.file("extdata", "subset_CosmicCLP_MutantExport.tsv.gz", package = "seqCAT") cosmic_samples <- list_cosmic(file)