read_cosmic {seqCAT} | R Documentation

## Read COSMIC SNV data

### 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

    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

    # 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)

[Package seqCAT version 1.2.1 Index]