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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Details

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

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