GenerateSyntheticExposures: Create synthetic exposures based given parameters

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

Create synthetic exposures based given parameters

Description

Create synthetic exposures based given parameters

Usage

GenerateSyntheticExposures(
  sig.params,
  num.samples = 10,
  name = "synthetic",
  sig.matrix = NULL,
  distribution = NULL,
  round.exposure = TRUE
)

Arguments

sig.params	Parameters from GetSynSigParamsFromExposures or another source. Should be a matrix or data frame with one column for each signature and the following rows: For log normal distribution, prob The proportion of tumors with the signature. mean The mean(log_10(number of mutations)). stdev The stdev(log_10(number of mutations)). For negative binomial distribution, prob The proportion of tumors with the signature. size Dispersion parameter. mu Mean. The rownames need to be the column names of a signature catalog.
num.samples	Number of samples to generate
name	Prefix for sample identifiers in the simulated dataset
sig.matrix	Signature matrix to construct synthetic tumors
distribution	Probability distribution used to generate synthetic exposures due to active mutational signatures. Can be neg.binom which stands for negative binomial distribution. If NULL (Default), then this function uses log normal distribution with base 10.
round.exposure	Whether the exposures should be rounded to an integer. Set as FALSE only when reproducing legacy data sets.

Value

A matrix with the rows being each signature and the columns being generated samples. Each entry is the count of mutations due to one signature in one sample.

steverozen/SynSigGen documentation built on April 1, 2022, 8:54 p.m.