SignatureFit_withBootstrap: Mutational Signatures Fit with Bootstrap (deprecated)

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

Mutational Signatures Fit with Bootstrap (deprecated)

Description

This function is deprecated. You can still use it, but we advise to use the function Fit instead, which provides a unified interface for basic signature fit with/without bootstrap. Fit a given set of mutational signatures into mutational catalogues to extimate the activty/exposure of each of the given signatures in the catalogues. Implementation of method similar to Huang et al. 2017, Detecting presence of mutational signatures with confidence, which uses a bootstrap apporach to calculate the empirical probability of an exposure to be larger or equal to a given threshold (i.e. 5 This probability can be used to decide which exposures to remove from the initial fit, thus increasing the sparsity of the exposures.

Usage

SignatureFit_withBootstrap(
  cat,
  signature_data_matrix,
  nboot = 100,
  exposureFilterType = "fixedThreshold",
  giniThresholdScaling = 10,
  giniThresholdScaling_nmuts = -1,
  threshold_percent = 5,
  threshold_nmuts = -1,
  threshold_p.value = 0.05,
  method = "KLD",
  bf_method = "CosSim",
  alpha = -1,
  verbose = TRUE,
  doRound = FALSE,
  nparallel = 1,
  n_sa_iter = 500,
  randomSeed = NULL,
  showDeprecated = TRUE
)

Arguments

cat	catalogue matrix, patients as columns, channels as rows
signature_data_matrix	signatures, signatures as columns, channels as rows
nboot	number of bootstraps to use, more bootstraps more accurate results
exposureFilterType	use either fixedThreshold or giniScaledThreshold. When using fixedThreshold, exposures will be removed based on a fixed percentage with respect to the total number of mutations (threshold_percent will be used). When using giniScaledThreshold each signature will used a different threshold calculated as (1-Gini(signature))*giniThresholdScaling
giniThresholdScaling	scaling factor for the threshold type giniScaledThreshold, which is based on the Gini score of a signature. The threshold is computed as (1-Gini(signature))*giniThresholdScaling, and will be used as a percentage of mutations in a sample that the exposure of "signature" need to be larger than. Set it to -1 to deactivate.
giniThresholdScaling_nmuts	scaling factor for the threshold type giniScaledThreshold, which is based on the Gini score of a signature. The threshold is computed as (1-Gini(signature))*giniThresholdScaling_nmuts, and will be used as number of mutations in a sample that the exposure of "signature" need to be larger than. Set to -1 to deactivate.
threshold_percent	threshold in percentage of total mutations in a sample, only exposures larger than threshold are considered. Set it to -1 to deactivate.
threshold_nmuts	threshold in number of mutations in a sample, only exposures larger than threshold are considered.Set it to -1 to deactivate.
threshold_p.value	p-value to determine whether an exposure is above the threshold_percent. In other words, this is the empirical probability that the exposure is lower or equal than the threshold
method	KLD or NNLS or SA
bf_method	bleeding filter method, one of KLD or CosSim, only if bleeding filter is used (alpha>-1)
alpha	set alpha to -1 to avoid Bleeding Filter
verbose	use FALSE to suppress messages
doRound	round the exposures to the closest integer
nparallel	to use parallel specify >1
n_sa_iter	set max Simulated Annealing iterations if method==SA
randomSeed	set an integer random seed
showDeprecated	set to FALSE to switch off the deprecated warning messsage

Value

returns the activities/exposures of the signatures in the given sample and other information, such as p-values and exposures of individual bootstrap runs.

References

Huang, X., Wojtowicz, D., & Przytycka, T. M. (2017). Detecting Presence Of Mutational Signatures In Cancer With Confidence. bioRxiv, (October). https://doi.org/10.1101/132597

Examples

res <- SignatureFit_withBootstrap(catalogues,signature_data_matrix)

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