read_cosmic: Read COSMIC data

In seqCAT: High Throughput Sequencing Cell Authentication Toolkit

Description

Read COSMIC sample-specific mutational data.

Usage

read_cosmic(file_path, sample_name = NULL, primary_site = NULL)

Arguments

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).

Details

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.

Value

A dataframe with COSMIC SNVs.

Examples

# 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")

seqCAT documentation built on Nov. 8, 2020, 7:36 p.m.