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Write the mutation calling file to input into the SigProfiler Assignment web application.

Source: R/write_sigprofiler_input.R
write_mutation_calling_file.Rd

Creates a .txt file from mutation data that can be used for mutational signatures analysis using the SigProfiler Assignment web application. Currently only supports SBS analysis i.e. snvs.

Usage

write_mutation_calling_file(
  mutation_data,
  project_name = "Example",
  project_genome = "GRCm38",
  output_path = NULL
)

Arguments

mutation_data

The object containing the mutation data. The output of import_mut_data() or import_vcf_data().

project_name

The name of the project. Default is "Example".

project_genome

The reference genome to use. (e.g., Human: GRCh38, Mouse mm10: GRCm38)

output_path

The path to save the output file. If NULL, files will be saved in the current working directory. Default is NULL.

Value

a .txt file that can be uploaded to the SigProfiler Assignment web application (https://cancer.sanger.ac.uk/signatures/assignment/) as a "Mutational calling file".

Details

Mutations will be be filtered for SNVs. Mutations flagged in filter_mut will be excluded from the output.

Examples

if (requireNamespace("MutSeqRData", quietly = TRUE)) {
  library(ExperimentHub)
  eh <- ExperimentHub()
  example_data <- eh[["EH9861"]]

  temp_output <- tempdir()
  write_mutation_calling_file(
    mutation_data = example_data,
    project_name = "Example",
    project_genome = "GRCm38",
    output_path = temp_output
  )
  list.files(temp_output)
  # The file is saved in the temporary directory
  # To view the file, use the following code:
  ## output_file <- file.path(temp_output, "mutation_calling_file.txt")
  ## file.show(output_file
}