# Copy number calling and SNV classification using targeted short read sequencing

## Documentation for package ‘PureCN’ version 1.8.1

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

## Help Pages

annotateTargets | Annotate targets with gene symbols
autoCurateResults | Heuristics to find the best purity/ploidy solution.
bootstrapResults | Filter unlikely purity/ploidy solutions
calculateBamCoverageByInterval | Function to calculate coverage from BAM file
calculateGCContentByInterval | Calculates GC content by interval
calculateLogRatio | Calculate coverage log-ratio of tumor vs. normal
calculatePowerDetectSomatic | Power calculation for detecting somatic mutations
callAlterations | Calling of amplifications and deletions
callAlterationsFromSegmentation | Calling of amplifications and deletions from segmentations
callLOH | Get regions of LOH
callMutationBurden | Call mutation burden
centromeres | A list of data.frames containing centromere positions.
correctCoverageBias | Correct for GC bias
createCurationFile | Create file to curate PureCN results
createNormalDatabase | Create database of normal samples
createSNPBlacklist | Create SNP black list
createTargetWeights | Calculate target weights
filterTargets | Remove low quality targets
filterVcfBasic | Basic VCF filter function
filterVcfMuTect | Filter VCF MuTect
filterVcfMuTect2 | Filter VCF MuTect2
findBestNormal | Find best normal sample in database
findFocal | Find focal amplifications
getDiploid | Function to extract diploid solutions.
getSexFromCoverage | Get sample sex from coverage
getSexFromVcf | Get sample sex from a VCF file
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-defunct | Defunct functions in package 'PureCN'
PureCN-deprecated | Deprecated functions in package 'PureCN'
purecn.example.output | Example output
readCoverageFile | Read coverage file
readCoverageGatk | Read GATK coverage files
readCurationFile | Read curation file
runAbsoluteCN | Run PureCN implementation of ABSOLUTE
segmentationCBS | CBS segmentation
segmentationPSCBS | PSCBS segmentation
setMappingBiasVcf | Set Mapping Bias VCF
setPriorVcf | Set Somatic Prior VCF