Write the mutation calling file to input into the SigProfiler Assignment web application.
Source:R/write_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 data consists of 24 mouse bone marrow
# samples exposed to three doses of BaP alongside vehicle controls.
# Libraries were sequenced with Duplex Sequencing using
# the TwinStrand Mouse Mutagenesis Panel which consists of 20 2.4kb
# targets = 48kb of sequence. Example data can be retrieved from
# MutSeqRData, an ExperimentHub data package:
## library(ExperimentHub)
## eh <- ExperimentHub()
## query(eh, "MutSeqRData")
# The data is a subset of variants from the target chr1
# from samples of the high dose group (50mg).
example_data <- readRDS(system.file("extdata", "Example_files",
"variants_subset_d50_chr1.rds",
package = "MutSeqR")
)
write_mutation_calling_file(
mutation_data = example_data,
project_name = "Example",
project_genome = "GRCm38",
output_path = tempdir()
)
list.files(tempdir())
#> [1] "bslib-06dfa953f10b44af4b6ca2dc86bfa180"
#> [2] "downlit"
#> [3] "file21df114437c5"
#> [4] "file21df35e60300"
#> [5] "file21df4a34f7e3"
#> [6] "file21df4d78e56f"
#> [7] "libloc_187_10f1dc1f01615a9f.rds"
#> [8] "libloc_192_4da063ac4afb603c.rds"
#> [9] "libloc_192_5fc0888d6df7bedc.rds"
#> [10] "libloc_201_893962b1c5113ec4.rds"
#> [11] "mutation_calling_file.txt"
#> [12] "repos_https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.23%2Fdata%2Fannotation%2Fsrc%2Fcontrib.rds"
#> [13] "temp_libpath21df27f322a8"
#> [14] "test_list.xlsx"
#> [15] "test_single.xlsx"
# The file is saved in the temporary directory
# To view the file, use the following code:
## output_file <- file.path(tempdir(), "mutation_calling_file.txt")
## file.show(output_file)