Package: PureCN 2.13.0

Markus Riester

PureCN: Copy number calling and SNV classification using targeted short read sequencing

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

Authors:Markus Riester [aut, cre], Angad P. Singh [aut]

PureCN_2.13.0.tar.gz
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PureCN.pdf |PureCN.html✨
PureCN/json (API)
NEWS

# Install 'PureCN' in R:

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

Bug tracker:https://github.com/lima1/purecn/issues

Datasets:

centromeres - A list of data.frames containing centromere positions.
purecn.DNAcopy.bdry - DNAcopy boundary data
purecn.example.output - Example output

On BioConductor:PureCN-2.13.0(bioc 3.21)PureCN-2.12.0(bioc 3.20)

copynumbervariation software sequencing variantannotation variantdetection coverage immunooncology bioconductor-package cell-free-dna copy-number loh tumor-heterogeneity tumor-mutational-burden tumor-purity

9.82 score 127 stars 52 scripts 402 downloads 11 mentions 43 exports 97 dependencies

Last updated 20 days agofrom:cb8d0f6c89. Checks:OK: 3 WARNING: 2 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	OK	Oct 31 2024
R-4.5-linux	OK	Oct 31 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

Exports:adjustLogRatio annotateTargets bootstrapResults calculateBamCoverageByInterval calculateLogRatio calculateMappingBiasGatk4 calculateMappingBiasVcf calculatePowerDetectSomatic calculateTangentNormal callAlterations callAlterationsFromSegmentation callAmplificationsInLowPurity callCIN callLOH callMutationBurden correctCoverageBias createCurationFile createNormalDatabase filterIntervals filterVcfBasic filterVcfMuTect filterVcfMuTect2 findFocal getSexFromCoverage getSexFromVcf plotAbs poolCoverage predictSomatic preprocessIntervals processMultipleSamples readAllelicCountsFile readCoverageFile readCurationFile readIntervalFile readLogRatioFile readSegmentationFile runAbsoluteCN segmentationCBS segmentationGATK4 segmentationHclust segmentationPSCBS setMappingBiasVcf setPriorVcf

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools colorspace cpp11 crayon curl data.table DBI DelayedArray DNAcopy fansi farver fastmap formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png R6 RColorBrewer RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow SparseArray SummarizedExperiment sys tibble UCSC.utils utf8 VariantAnnotation vctrs VGAM viridisLite withr XML XVector yaml zlibbioc

PureCN best practices

Markus Riester

Rendered fromQuick.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-12-11
Started: 2019-08-31

Overview of the PureCN R package

Rendered fromPureCN.Rnwusingknitr::knitron Oct 31 2024.

Last update: 2023-12-11
Started: 2016-04-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Adjust tumor vs. normal coverage log ratio for tumor purity and ploidy	adjustLogRatio
Annotate targets with gene symbols	annotateTargets
Bootstrapping variant fits	bootstrapResults
Function to calculate coverage from BAM file	calculateBamCoverageByInterval
Calculate coverage log-ratio of tumor vs. normal	calculateLogRatio
Calculate Mapping Bias from GATK4 GenomicsDB	calculateMappingBiasGatk4
Calculate Mapping Bias	calculateMappingBiasVcf
Power calculation for detecting somatic mutations	calculatePowerDetectSomatic
Calculate tangent normal	calculateTangentNormal
Calling of amplifications and deletions	callAlterations
Calling of amplifications and deletions from segmentations	callAlterationsFromSegmentation
Calling of amplifications in low purity samples	callAmplificationsInLowPurity
Call Chromosomal Instability	callCIN
Get regions of LOH	callLOH
Call mutation burden	callMutationBurden
A list of data.frames containing centromere positions.	centromeres
Correct for library-specific coverage biases	correctCoverageBias
Create file to curate PureCN results	createCurationFile
Create database of normal samples	createNormalDatabase
Remove low quality intervals	filterIntervals
Basic VCF filter function	filterVcfBasic
Filter VCF MuTect	filterVcfMuTect
Filter VCF MuTect2	filterVcfMuTect2
Find focal amplifications	findFocal
Get sample sex from coverage	getSexFromCoverage
Get sample sex from a VCF file	getSexFromVcf
Plots for analyzing PureCN solutions	plotAbs
Pool coverage from multiple samples	poolCoverage
Predict germline vs. somatic status	predictSomatic
Preprocess intervals	preprocessIntervals
Multi sample normalization and segmentation	processMultipleSamples
Defunct functions in package 'PureCN'	PureCN-defunct
Deprecated functions in package 'PureCN'	PureCN-deprecated
DNAcopy boundary data	purecn.DNAcopy.bdry
Example output	purecn.example.output
Read allelic counts file	readAllelicCountsFile
Read coverage file	readCoverageFile
Read curation file	readCurationFile
Read interval file	readIntervalFile
Read file containing interval-level log2 tumor/normal ratios	readLogRatioFile
Read file containing segmentations	readSegmentationFile
Run PureCN implementation of ABSOLUTE	runAbsoluteCN
CBS segmentation	segmentationCBS
GATK4 ModelSegments segmentation function	segmentationGATK4
Minimal segmentation function	segmentationHclust
PSCBS segmentation	segmentationPSCBS
Set Mapping Bias VCF	setMappingBiasVcf
Set Somatic Prior VCF	setPriorVcf