PureCN v1.0.3

by Markus Riester

Estimating tumor purity, ploidy, LOH, and SNV status using hybrid capture NGS data

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

Functions in PureCN

Name	Description
filterVcfMuTect	Filter VCF MuTect
chr.hash	A data.frame of chromosome names.
correctCoverageBias	Correct for GC bias
createSNPBlacklist	Create SNP black list
findBestNormal	Find best normal sample in database
findFocal	Find focal amplifications
setPriorVcf	Set Somatic Prior VCF
predictSomatic	Predict germline vs. somatic status
getSexFromCoverage	Get sample sex from coverage
purecn.example.output	Example output
createNormalDatabase	Create database of normal samples
segmentationPSCBS	PSCBS segmentation
segmentationCBS	CBS segmentation
readCurationFile	Read curation file
runAbsoluteCN	Run PureCN implementation of ABSOLUTE
poolCoverage	Pool coverage from multiple samples
plotAbs	Plots for analyzing PureCN solutions
readCoverageGatk	Read GATK coverage files
createCurationFile	Create file to curate PureCN results
plotBestNormal	Plot the PCA of tumor and its best normal(s)
filterVcfBasic	Basic VCF filter function
createExonWeightFile	Calculate exon weights
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Type	Package
Date	2016-06-04
VignetteBuilder	knitr
License	Artistic-2.0
biocViews	CopyNumberVariation, Software, Sequencing, VariantAnnotation, VariantDetection
NeedsCompilation	no
Packaged	2016-04-14 21:52:04 UTC; riestma1

depends	base (>= 3.3) , DNAcopy , R (>= 3.3) , VariantAnnotation (>= 1.14.1)
suggests	BiocGenerics , BiocStyle , knitr , PSCBS , RUnit
imports	data , data.table , GenomeInfoDb , GenomicRanges (>= 1.20.3) , graphics , grDevices , IRanges (>= 2.2.1) , RColorBrewer , S4Vectors , stats , SummarizedExperiment , utils
Contributors	Markus Riester

PureCN v1.0.3

Estimating tumor purity, ploidy, LOH, and SNV status using hybrid capture NGS data

Functions in PureCN

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