simpleCatalogueSimulation: simpleCatalogueSimulation

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

simpleCatalogueSimulation

Description

This is a simple function that produces simulated mutational catalgoues and exposures, given a set of mutational signatures. Each catalogue is simulated as follows. The total number of mutations in a catalogue is sampled uniformely in the log space, and the results exponetiated, so that most samples have total mutations closer to min_mutations than max_mutations. exposures for common signatures and rare signatures (if any) are then sampled uniformely, and the result scaled so that the sum of the mutations corresponds to the number sampled initially.

Usage

simpleCatalogueSimulation(
  commonSignatures,
  rareSignatures = NULL,
  ngenomes = 50,
  ncommon_signatures_per_sample = 5,
  nsamplesWrareSigs = 10,
  maxRareSigsPerSample = 1,
  min_mutations = 1000,
  max_mutations = 50000,
  randomSeed = NULL
)

Arguments

commonSignatures	mutational signatures matrix with the signatures to be considered common
rareSignatures	mutational signatures matrix with the signatures to be considered rare, can be omitted
ngenomes	how many mutational catalogues should be simulated
ncommon_signatures_per_sample	how many common signatures should be present in each sample
nsamplesWrareSigs	how many samples should have rare signatures
maxRareSigsPerSample	the maxiumum number of rare signature that can be present in a sample
min_mutations	minimum number of mutations in a sample
max_mutations	maximum number of mutations in a sample
randomSeed	set a random seed for reproducibility

Value

catalogues, signatures and exposures of simulated data

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.