Package: decompTumor2Sig 2.21.0

Rosario M. Piro

decompTumor2Sig: Decomposition of individual tumors into mutational signatures by signature refitting

Uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.

Authors:Rosario M. Piro [aut, cre], Sandra Krueger [ctb]

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decompTumor2Sig.pdf |decompTumor2Sig.html✨
decompTumor2Sig/json (API)
NEWS

# Install 'decompTumor2Sig' in R:

install.packages('decompTumor2Sig', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rmpiro/decomptumor2sig/issues

On BioConductor:decompTumor2Sig-2.21.0(bioc 3.20)decompTumor2Sig-2.20.0(bioc 3.19)

bioconductor-package

24 exports 1 stars 4.78 score 103 dependencies 1 dependents 2 mentions 10 scripts 327 downloads

Last updated 5 months agofrom:559c87fa41. Checks:OK: 2 NOTE: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 05 2024
R-4.5-win	NOTE	Sep 05 2024
R-4.5-linux	OK	Sep 05 2024
R-4.4-win	NOTE	Sep 05 2024
R-4.4-mac	NOTE	Jul 30 2024
R-4.3-win	NOTE	Aug 06 2024
R-4.3-mac	NOTE	Jul 31 2024

Exports:adjustSignaturesForRegionSet composeGenomesFromExposures computeExplainedVariance convertAlexandrov2Shiraishi convertGenomesFromVRanges decomposeTumorGenomes determineSignatureDistances downgradeShiraishiSignatures evaluateDecompositionQuality getGenomesFromMutFeatData getSignaturesFromEstParam isAlexandrovSet isExposureSet isShiraishiSet isSignatureSet mapSignatureSets plotDecomposedContribution plotExplainedVariance plotMutationDistribution readAlexandrovSignatures readGenomesFromMPF readGenomesFromVCF readShiraishiSignatures sameSignatureFormat

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg19 cachem cellranger cli codetools colorspace cpp11 crayon curl data.table DBI DelayedArray fansi farver fastmap formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggseqlogo glue gridExtra gtable hms httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png prettyunits progress quadprog R6 RColorBrewer Rcpp RCurl readxl rematch restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow SparseArray SummarizedExperiment sys tibble TxDb.Hsapiens.UCSC.hg19.knownGene UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr XML XVector yaml zlibbioc

A brief introduction to decompTumor2Sig

Rosario Michael Piro

Rendered fromdecompTumor2Sig.Rmdusingknitr::rmarkdownon Sep 05 2024.

Last update: 2021-03-26
Started: 2018-07-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
decompTumor2Sig - Decomposition of individual tumors into mutational signatures by signature refitting	decompTumor2Sig-package decompTumor2Sig
Adjust (normalize) signatures for a set of genomic regions.	adjustSignaturesForRegionSet
Compose tumor genomes from exposures.	composeGenomesFromExposures
Compute the explained variance.	computeExplainedVariance
Convert Alexandrov-type signatures to Shiraishi signatures	convertAlexandrov2Shiraishi
Convert genomes from a 'VRanges' object	convertGenomesFromVRanges
Decompose tumor genomes into mutational signatures	decomposeTumorGenomes
Determine differences between a given signature and a set of target signatures.	determineSignatureDistances
Downgrade Shiraishi-type signatures.	downgradeShiraishiSignatures
Evaluate tumor decomposition quality.	evaluateDecompositionQuality
Get genomes (mutation frequencies) from 'MutationFeatureData'.	getGenomesFromMutFeatData
Get signatures from an 'EstimatedParameters' object.	getSignaturesFromEstParam
isAlexandrovSet	isAlexandrovSet
isExposureSet	isExposureSet
isShiraishiSet	isShiraishiSet
isSignatureSet	isSignatureSet
Map one signature set to another.	mapSignatureSets
Plot the decomposition (contributions/exposures) of a tumor genome.	plotDecomposedContribution
Plot the explained variance as a function of the number of signatures	plotExplainedVariance
Plot mutation frequency data of a mutational signature or tumor genome.	plotMutationDistribution
Read Alexandrov-type signatures (COSMIC format).	readAlexandrovSignatures
Read tumor genomes from an MPF file (Mutation Position Format).	readGenomesFromMPF
Read tumor genomes from a VCF file (Variant Call Format).	readGenomesFromVCF
Read a set of Shiraishi signatures.	readShiraishiSignatures
sameSignatureFormat	sameSignatureFormat