GenerateListOfSigParams: Generate a list of signature parameters for different cancer...

In steverozen/SynSigGen: Create Catalogs of Synthetic Mutational Spectra

Generate a list of signature parameters for different cancer types from real exposure

Description

Generate a list of signature parameters for different cancer types from real exposure

Usage

GenerateListOfSigParams(
  real.exposures,
  cancer.types,
  distribution = NULL,
  verbose = 0,
  sig.params = NULL
)

Arguments

real.exposures	A matrix of real exposures.
cancer.types	A vector of character strings denoting different cancer types. This function will search real.exposures for exposures from tumors matching these strings. See PCAWG7::CancerTypes() for example.
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.
verbose	If > 0 cat various messages.
sig.params	Empirical signature parameters generated using real exposures irrespective of their cancer types. If there is only one tumor having a signature in a cancer type in real.exposures, we cannot fit the distribution to only one data point. Instead, we will use the empirical parameter size from sig.params. Users can use SynSigGen:::GetSynSigParamsFromExposuresOld to generate their own signature parameters. If NULL(default), this function uses the PCAWG7 empirical signature parameters. See signature.params for more details.

Note

This function calls GetSynSigParamsFromExposures.

Examples

# Generate a list of signature parameters for Indel (ID) using negative binomial distribution
real.exposures.ID <- PCAWG7::exposure$PCAWG$ID
cancer.types <- PCAWG7::CancerTypes()[1:5]
sig.params <- SynSigGen::signature.params$ID
ID.sig.params <-
  GenerateListOfSigParams(real.exposures = real.exposures.ID,
                          cancer.types = cancer.types,
                          distribution = "neg.binom",
                          sig.params = sig.params
 )

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