finaliseCommonRareSignatureExposures: Finalise Common and Rare Signature Exposures

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

Finalise Common and Rare Signature Exposures

Description

This function is part of the pipeline for the extraction of rare signatures. After the rare signatures have been extracted and the corresponding samples identified using the rareSignatureExtraction function, this function fits the common and rare signatures into the sample catalogues and reports also a comparison between the normalised error withvs without rare signatures.

Usage

finaliseCommonRareSignatureExposures(
  outfileRoot,
  catalogues,
  commonSigs,
  listofsignatures = NULL,
  listofsamples = NULL,
  nboot = 200,
  threshold_percent = 5,
  threshold_p.value = 0.05,
  min_sample_muts = 100,
  nparallel = 1
)

Arguments

outfileRoot	output directory and base file name, for example outdir/BaseName. Multiple output files will be generated with filenames the chosen BaseName as prefix.
catalogues	original catalogues, channels as rows and samples as columns
commonSigs	common mutational signatures used for fitting, channels as rows, signatures as columns
listofsignatures	listofsignatures object obtained from the rareSignatureExtraction function. It contains the rare signatures extracted
listofsamples	listofsamples object obtained from the rareSignatureExtraction function. It contains the samples that have each of the rare signatures extracted
nboot	number of bootstraps for the signature fit
threshold_percent	minimum percentage of mutations in a sample that should be assigned to a signature
threshold_p.value	p-value to decide whether a signature exposure is statistically higher then the threshold_percent
min_sample_muts	minimum number of mutations in a sample to perform signature analysis. If a sample has less than min_sample_muts mutations, then all signature exposures are set to zero and all mutations are unsassigned
nparallel	number of parallel processes to use for the signature fit

Value

exposures and errors for the signature fit using common+rare signatures and common only signatures

Examples

resUnexpl <- unexplainedSamples(catalogues=catalogues,
                                sigs=signatures)
significant_residuals <- resUnexpl$all_residuals[,resUnexpl$which_significant]
clusterResiduals <- cataloguesClustering(significant_residuals,
                                         nclusters = 1:5)
resObj <- rareSignatureExtraction(catalogues=catalogues,
                                  commonSignatures=signatures,
                                  commonExposures=resUnexpl$exposures,
                                  residuals=resUnexpl$all_residuals,
                                  unexpl_samples=resUnexpl$unexplSamples,
                                  clusters=clusterResiduals$clusters_table[,"3"],
                                  useclusters=list=(c(1),c(3)),
                                  maxiter=c(100,1000))
finaliseCommonRareSignatureExposures(outfileRoot = "outdir/BaseName",
                                     catalogues = catalogues,
                                     commonSigs = signatures,
                                     listofsignatures = resObj$listofsignatures,
                                     listofsamples = resObj$listofsamples)

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