mm_fit_signatures: Mutational signature fitting with mmsig

In bachisiozic/mmsig: A Mutational Signature Fitting Tool for Hematological Cancers

Description

Mutational signature fitting with mmsig

Usage

mm_fit_signatures(
  muts.input,
  sig.input,
  input.format = "vcf",
  sample.sigt.profs = NULL,
  bootstrap = FALSE,
  iterations = 1000,
  strandbias = FALSE,
  refcheck = TRUE,
  cos_sim_threshold = 0.01,
  force_include = c("SBS1", "SBS5"),
  dbg = FALSE
)

Arguments

muts.input	mutation input data frame as specified under input.format
sig.input	mutational signature reference with mutational classes as rows and signature exposures as columns: Substitution.Type, Trinucleotide, signature.1, ... signature.n
input.format	vcf: five column vcf-like data frame with the following columns: sample, chr (e.g. chr1), pos, ref, alt. classes: samples as columns and the 96 mutational classes as rows
sample.sigt.profs	NULL = use all signatures provided in the reference. Optionally provide list with signatures to consider for each sample
bootstrap	TRUE/FALSE for whether bootstrapping is to be performed
iterations	number of bootstrapping iterations to perform (only if bootstrap == TRUE)
strandbias	TRUE/FALSE for whether transcriptional strand bias should be tested for (only for vcf-like input format)
refcheck	check that input mutational catalog (if vcf-format) is aligned to hg19
cos_sim_threshold	cosine similarity threshold below which signatures are removed from the final profile
force_include	vector with the names of signatures to always keep in the final profile of every sample
dbg	FALSE = silent; TRUE = verbose

Value

mutational signature fitting results for all samples

bachisiozic/mmsig documentation built on Feb. 16, 2021, 12:03 a.m.