read_cosmic: Read COSMIC data
In fasterius/seqCAT: High Throughput Sequencing Cell Authentication Toolkit

Description Usage Arguments Details Value Examples

Read COSMIC sample-specific mutational data.

1	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")