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.
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The CosmicCLP_MutantExport.tsv.gz file (path).
The cell line to be investigated (character).
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.
A GRanges object with COSMIC SNVs.
A vector of cell line names
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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)
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