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PureCN (version 1.0.3)

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

Description

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.

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Version

Version

1.0.3

License

Artistic-2.0

Maintainer

Markus Riester

Last Published

February 15th, 2017

Functions in PureCN (1.0.3)

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