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

## Documentation for package ‘PureCN’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

chr.hash | A data.frame of chromosome names.
correctCoverageBias | Correct for GC bias
createCurationFile | Create file to curate PureCN results
createExonWeightFile | Calculate exon weights
createNormalDatabase | Create database of normal samples
createSNPBlacklist | Create SNP black list
filterVcfBasic | Basic VCF filter function
filterVcfMuTect | Filter VCF MuTect
findBestNormal | Find best normal sample in database
findFocal | Find focal amplifications
getSexFromCoverage | Get sample sex from coverage
plotAbs | Plots for analyzing PureCN solutions
plotBestNormal | Plot the PCA of tumor and its best normal(s)
poolCoverage | Pool coverage from multiple samples
predictSomatic | Predict germline vs. somatic status
purecn.example.output | Example output
readCoverageGatk | Read GATK coverage files
readCurationFile | Read curation file
runAbsoluteCN | Run PureCN implementation of ABSOLUTE
segmentationCBS | CBS segmentation
segmentationPSCBS | PSCBS segmentation
setPriorVcf | Set Somatic Prior VCF