read_cosmic {seqCAT} | R Documentation

## Read COSMIC data

### 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")

[Package seqCAT version 1.10.0 Index]