read_cosmic: Read COSMIC SNV data

Description Usage Arguments Details Value Examples

View source: R/read_cosmic.R

Description

Read COSMIC cell line-specific mutational data.

This function lists the available cell lines in the provided CosmicCLP_MutantExport.tsv.gz file, and take 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 cell line is listed in COSMIC or not.

Usage

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read_cosmic(file_path, cell_line)

list_cosmic(file_path)

Arguments

file_path

The CosmicCLP_MutantExport.tsv.gz file (path).

cell_line

The cell line to be investigated (character).

Details

This function reads the "CosmicCLP_MutantExport.tsv.gz" file obtained from COSMIC and returns a GRanges object with all the listed mutations for the specified cell line, 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.

A vector of cell line names

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 HCT116 cell line
cosmic_hct116 <- read_cosmic(file, "HCT116")
file <- system.file("extdata",
                    "subset_CosmicCLP_MutantExport.tsv.gz",
                    package = "seqCAT")
cell_lines <- list_cosmic(file)

seqCAT documentation built on May 30, 2018, 6 p.m.