exposureDistributionBarplot: Distribution of Signatures in Samples

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

Distribution of Signatures in Samples

Description

Given a catalogue of samples and an exposures table, compute the relative amount of each signature in each sample and the unassigned mutations. Also cluster the samples with hierarchical clustering with average linkage and order the samples according to the clustering. Optionally, plot to file.

Usage

exposureDistributionBarplot(fileout = NULL, catalogue, exposures)

Arguments

fileout	if specified, generate a plot, otherwise no plot is generated, use extension png or jpg
catalogue	original catalogue, channels as rows and samples as columns
exposures	exposures/activities of signatures in each sample. Signatures as rows, samples as columns

Value

list with to objects: the matrix of the distribution of the signatures in the samples and the hierarchical clustering object

Examples

res <- SignatureFit_withBootstrap(cat = catalogue,
                  signature_data_matrix = cosmic30,
                  nboot = 5,
                  threshold_percent = 0.1,
                  threshold_p.value = 0.1)
distribution_object <- exposureDistributionBarplot(catalogue=catalogue,
                  exposures=res$E_median_filtered)

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