GenerateSynExposureOneSample: Using parameters given to generate exposures for synthetic...

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

Using parameters given to generate exposures for synthetic tumors

Description

Using parameters given to generate exposures for synthetic tumors

Usage

GenerateSynExposureOneSample(
  tumor,
  sig.interest,
  burden.per.sig,
  sd.per.sig,
  sig.matrix = NULL,
  distribution = NULL,
  sig.params = NULL,
  round.exposure = TRUE
)

Arguments

tumor	Signature presence matrix or exposure matrix for a tumor. It has only one row, and K (# of signatures) columns. Value in each column is the presence flag for a mutational signature: the value can be non-zero(signature is present) or 0(absent). The name of each column should be the name of a signature.
sig.interest	Names of mutational signatures you want to use to generate exposures. It can be all, or part of signatures in colnames(tumor).
burden.per.sig	Mean mutation burden a log10 of the counts of mutations per megabase. It has one row, and K columns. Each column name refers to a mutational signature.
sd.per.sig	standard deviation of mutation burden. It has one row, and K columns. Each column name refers to a mutational signature.
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.
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.
round.exposure	Whether the exposures should be rounded to an integer. Set as FALSE only when reproducing legacy data sets.

Details

Determine the intensity of each mutational signature in a tumor, returning the number of mutations using the mean mutation burden per signature and the std dev

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