Package: SparseSignatures 2.17.0

Luca De Sano

SparseSignatures: SparseSignatures

Point mutations occurring in a genome can be divided into 96 categories based on the base being mutated, the base it is mutated into and its two flanking bases. Therefore, for any patient, it is possible to represent all the point mutations occurring in that patient's tumor as a vector of length 96, where each element represents the count of mutations for a given category in the patient. A mutational signature represents the pattern of mutations produced by a mutagen or mutagenic process inside the cell. Each signature can also be represented by a vector of length 96, where each element represents the probability that this particular mutagenic process generates a mutation of the 96 above mentioned categories. In this R package, we provide a set of functions to extract and visualize the mutational signatures that best explain the mutation counts of a large number of patients.

Authors:Daniele Ramazzotti [aut], Avantika Lal [aut], Keli Liu [ctb], Luca De Sano [cre, aut], Robert Tibshirani [ctb], Arend Sidow [aut]

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NEWS

# Install 'SparseSignatures' in R:
install.packages('SparseSignatures', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/danro9685/sparsesignatures/issues

Datasets:
  • background - Germline replication error
  • background2 - COSMIC replication error
  • cv_example - Example of results obtained with the function nmf.LassoCV on the counts input from Nik-Zainal, Serena, et al. (2016).
  • imported_data - Example of imported data from Nik-Zainal, Serena, et al. (2016).
  • lambda_range_example - Example of results obtained with the function evaluate.lambda.range on the counts input from Nik-Zainal, Serena, et al. (2016).
  • mutation_categories - Trinucleotides mutation categories
  • nmf_LassoK_example - Example of results obtained with the function nmf.LassoK on the counts input from Nik-Zainal, Serena, et al. (2016).
  • patients - Point mutations for 560 breast tumors
  • ssm560_reduced - A reduced version of the point mutations for 560 breast tumors in the format compatible with the import function
  • starting_betas_example - Example of results obtained with the function starting.betas.estimation on the counts input from Nik-Zainal, Serena, et al. (2016).

On BioConductor:SparseSignatures-2.17.0(bioc 3.21)SparseSignatures-2.16.0(bioc 3.20)

biomedicalinformaticssomaticmutation

6.42 score 11 stars 4 scripts 250 downloads 3 mentions 12 exports 95 dependencies

Last updated 4 months agofrom:f2c94d341a. Checks:1 OK, 7 NOTE. Indexed: yes.

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Exports:import.trinucleotides.countslambdaRangeAlphaEvaluationlambdaRangeBetaEvaluationnmfLassonmfLassoBootstrapnmfLassoCVpatients.plotsigAssignmentCVsigAssignmentEvaluationsigAssignmentLassosignatures.plotstartingBetaEstimation

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitopsBSgenomecliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydigestdoParallelfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegridBasegridExtragtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeNMFnnlassonnlsopensslpillarpkgconfigplyrR6RColorBrewerRcppRCurlregistryreshape2restfulrRhpcBLASctlRhtslibrjsonrlangrngtoolsRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

Introduction

Daniele Ramazzotti, Avantika Lal, Keli Liu, Luca De Sano, Robert Tibshirani, Arend Sidow

Rendered fromv1_introduction.rmdusingknitr::rmarkdownon Jan 31 2025.

Last update: 2023-04-10
Started: 2023-04-10

Using the package

Daniele Ramazzotti, Avantika Lal, Keli Liu, Luca De Sano, Robert Tibshirani, Arend Sidow

Rendered fromv2_using_the_package.rmdusingknitr::rmarkdownon Jan 31 2025.

Last update: 2023-04-10
Started: 2023-04-10