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

## Documentation for package ‘PureCN’ version 1.20.0

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

## Help Pages

annotateTargets | Annotate targets with gene symbols
bootstrapResults | Bootstrapping variant fits
calculateBamCoverageByInterval | Function to calculate coverage from BAM file
calculateIntervalWeights | Calculate interval weights
calculateLogRatio | Calculate coverage log-ratio of tumor vs. normal
calculateMappingBiasGatk4 | Calculate Mapping Bias from GATK4 GenomicsDB
calculateMappingBiasVcf | Calculate Mapping Bias
calculatePowerDetectSomatic | Power calculation for detecting somatic mutations
calculateTangentNormal | Calculate tangent normal
callAlterations | Calling of amplifications and deletions
callAlterationsFromSegmentation | Calling of amplifications and deletions from segmentations
callAmplificationsInLowPurity | Calling of amplifications in low purity samples
callCIN | Call Chromosomal Instability
callLOH | Get regions of LOH
callMutationBurden | Call mutation burden
centromeres | A list of data.frames containing centromere positions.
correctCoverageBias | Correct for library-specific coverage biases
createCurationFile | Create file to curate PureCN results
createNormalDatabase | Create database of normal samples
filterIntervals | Remove low quality intervals
filterVcfBasic | Basic VCF filter function
filterVcfMuTect | Filter VCF MuTect
filterVcfMuTect2 | Filter VCF MuTect2
findFocal | Find focal amplifications
getSexFromCoverage | Get sample sex from coverage
getSexFromVcf | Get sample sex from a VCF file
plotAbs | Plots for analyzing PureCN solutions
poolCoverage | Pool coverage from multiple samples
predictSomatic | Predict germline vs. somatic status
preprocessIntervals | Preprocess intervals
processMultipleSamples | Multi sample normalization and segmentation
PureCN-defunct | Defunct functions in package 'PureCN'
PureCN-deprecated | Deprecated functions in package 'PureCN'
purecn.DNAcopy.bdry | DNAcopy boundary data
purecn.example.output | Example output
readCoverageFile | Read coverage file
readCurationFile | Read curation file
readLogRatioFile | Read file containing interval-level log2 tumor/normal ratios
readSegmentationFile | Read file containing segmentations
runAbsoluteCN | Run PureCN implementation of ABSOLUTE
segmentationCBS | CBS segmentation
segmentationHclust | Minimal segmentation function
segmentationPSCBS | PSCBS segmentation
setMappingBiasVcf | Set Mapping Bias VCF
setPriorVcf | Set Somatic Prior VCF