read_cosmic: Read COSMIC data

Description Usage Arguments Details Value Examples

View source: R/read_cosmic.R

Description

Read COSMIC sample-specific mutational data.

Usage

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read_cosmic(file_path, sample_name)

Arguments

file_path

The COSMIC data file path (path).

sample_name

The sample to be investigated (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 GRanges object with COSMIC SNVs.

Examples

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# 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. 1, 2018, 2:07 a.m.