tempoSig: Create 'tempoSig' object

In mskcc/tempoSig: Maximum Likelihood Fitting of Mutational Catalogs and De Novo Inference of Signatures

Create tempoSig object

Usage

tempoSig(data, signat = "v2")

Arguments

data	Input data of mutation catalog; samples in columns and mutation types in rows.
signat	Reference signatures table; default is COSMIC version 3 signatures. It can be a matrix of the table, the file name containing the table, or character code c('v2', 'SA','SP'), signifying COSMIC v2, sigAnalyzer, or SigProfiler references (the latter two are COSMIC v3).

Value

Object of class tempoSig.

Examples

set.seed(130)
data <- rmultinom(n = 5, size = 100, prob = rep(1,96))
rownames(data) <- trinucleotides()
colnames(data) <- paste0('S',seq(5))
s <- tempoSig(data)
data <- read.table(system.file('extdata', 'tcga-brca_catalog.txt',
                  package='tempoSig'), header=TRUE, sep='\t')
b <- tempoSig(data)

mskcc/tempoSig documentation built on Feb. 3, 2023, 8:35 a.m.