fun_load_mutation: Mutation data file loader
In MicroSEC: Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples

fun_load_mutation

R Documentation

Mutation data file loader

Description

This function attempts to load the mutation information file.

Usage

fun_load_mutation(
  mutation_file,
  sample_name,
  ref_genome,
  chr_no,
  simple_repeat_list = ""
)

Arguments

`mutation_file`	Path of the mutation information file.
`sample_name`	Sample name.
`ref_genome`	Reference genome for the data.
`chr_no`	Reference genome chromosome number (human=24, mouse=22).
`simple_repeat_list`	Optional, set simple repeat bed file path.

Value

df_mutation

Examples

fun_load_mutation(
  system.file("extdata", "mutation_list.tsv", package = "MicroSEC"),
  "sample",
  BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38,
  24
)

MicroSEC documentation built on Sept. 11, 2024, 6:06 p.m.