Write the mutation calling file to input into the SigProfiler Assignment web application.
Source:R/get_sigprofiler_input.R
write_mutation_calling_file.RdCreates 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
example_file <- system.file("extdata", "Example_files",
"example_mutation_data_filtered.rds",
package = "MutSeqR")
example_data <- readRDS(example_file)
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)
#> [1] "bslib-2ce9eb5d8d7866b4f2d82a9ef19eb08f"
#> [2] "downlit"
#> [3] "downloaded_packages"
#> [4] "file340d1842e06a"
#> [5] "file340d25a93e76"
#> [6] "file340d5cd46615"
#> [7] "file340d9ca38ff"
#> [8] "file340da33eb51"
#> [9] "libloc_177_9a667201821007d.rds"
#> [10] "libloc_182_ba3851d8a9100920.rds"
#> [11] "libloc_182_d3198563f59e5c50.rds"
#> [12] "mutation_calling_file.txt"
#> [13] "repos_https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.21%2Fbioc%2Fsrc%2Fcontrib.rds"
#> [14] "repos_https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.21%2Fbooks%2Fsrc%2Fcontrib.rds"
#> [15] "repos_https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.21%2Fdata%2Fannotation%2Fsrc%2Fcontrib.rds"
#> [16] "repos_https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.21%2Fdata%2Fexperiment%2Fsrc%2Fcontrib.rds"
#> [17] "repos_https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.21%2Fworkflows%2Fsrc%2Fcontrib.rds"
#> [18] "repos_https%3A%2F%2Fcran.rstudio.com%2Fsrc%2Fcontrib.rds"
#> [19] "repos_https%3A%2F%2Fpackagemanager.posit.co%2Fcran%2F__linux__%2Fnoble%2Flatest%2Fsrc%2Fcontrib.rds"
# 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