mutSigMapper-package: maps spectra to mutational signatures

In juliancandia/mutSigMapper: Mapping Spectra to Mutational Signatures Based on Shot-Noise Modeling

Description

Provides a quantitative, non-parametric assessment of statistical significance for the association between mutational signatures and observed spectra.

Details

Package:	mutSigMapper
Type:	Package
Version:	0.99.0
Date:	2020-10-05
License:	GPL-3

This package provides a full pipeline of analysis: mutSigMapper takes in spectra and sig data to assess the statistical significance of sample/signature associations via shot-noise modeling; plotSpectraCaterpillar generates caterpillar plots of signature weights for individual samples; plotSpectraHeatmap generates heatmap plots of spectra vs mutational signatures based on weights, cosine similarity, Jensen-Shannon divergence, or correlation; and export creates plain text output files for downstream processing. Example spectra from published sources are provided. Curated built-in signature compendia extracted de novo from large-scale analysis of cancer genomes and exomes (COSMIC) as well as from cell lines treated with known mutagens (Kucab et al, Cell 2019) are also provided.

Author(s)

Julian Candia
Maintainer: Julian Candia [e-mail]

References

COSMIC (Catalogue Of Somatic Mutations In Cancer), https://cancer.sanger.ac.uk/cosmic/signatures/index.tt

Kucab JE et al. A Compendium of Mutational Signatures of Environmental Agents, Cell 177, 821-836.e16 (2019).

Candia J. mutSigMapper: an R package to map spectra to mutational signatures based on shot-noise modeling, bioRxiv (2020).

See Also

mutSigMapper, plotSpectraCaterpillar, plotSpectraHeatmap, export.

Examples

data(spectra)
map = mutSigMapper(spectra)
plotSpectraCaterpillar(map,spectra.set="colon1")
cos_sim = plotSpectraHeatmap(map,type="cosine")
export(x=map,dest_dir=tempdir())

juliancandia/mutSigMapper documentation built on Oct. 19, 2020, 3:58 a.m.