read_cosmic {seqCAT} | R Documentation |
Read COSMIC sample-specific mutational data.
read_cosmic(file_path, sample_name = NULL, primary_site = NULL)
file_path |
The COSMIC data file path (path). |
sample_name |
Subset the data on sample name (character). |
primary_site |
Subset the data on primary tumour site (character). |
This function reads the COSMIC data files (e.g. "CosmicCLP_MutantExport.tsv.gz") and returns a GRanges object with all the listed mutations for the specified sample, which can then be use in downstream profile comparisons. Only non-duplicated (gene-level) SNVs are included in COSMIC profiles.
A dataframe with COSMIC SNVs.
# Path to COSMIC test data file <- system.file("extdata", "subset_CosmicCLP_MutantExport.tsv.gz", package = "seqCAT") # Read COSMIC test data for the HCT116 cell line cosmic_hct116 <- read_cosmic(file, "HCT116")