readSigsAsDf: Read multiple files outputed my mutSigExtractor into a data...

In UMCUGenetics/mutSigExtractor: Extracts SNV, indel, DBS, and SV signatures from vcf files.

Read multiple files outputed my mutSigExtractor into a data frame

Description

Read multiple files outputed my mutSigExtractor into a data frame

Usage

readSigsAsDf(dir = NULL, files = NULL, samples.as.rows = T, verbose = T, ...)

Arguments

dir	A directory from which to read the signatures/contexts
files	Alternatively, a list of file paths can also be specified
samples.as.rows	Samples as rows and signatures/contexts as columns?
verbose	Show file reading progress?
...	Arguments that can be pass to list.files() and read.table()

Value

A data frame

Examples

base_dir <- '/Users/lnguyen/hpc/cog_bioinf/cuppen/project_data/Luan_projects/CHORD/Breast_Organoids/matrices/'
contexts <- list(
   snv = readSigsAsDf(paste0(base_dir,'/snv_contexts')),
   indel = readSigsAsDf(paste0(base_dir,'/indel')),
   sv = readSigsAsDf(paste0(base_dir,'/sv_contexts'))
)

UMCUGenetics/mutSigExtractor documentation built on Aug. 30, 2024, 2:12 p.m.