This package estimates tumor purity, copy number, loss of heterozygosity (LOH), and status of single nucleotide variants (SNVs). PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection pipelines, and has support for tumor samples without matching normal samples.
|Date of publication||None|
|Maintainer||Markus Riester <email@example.com>|
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
centromeres: A list of data.frames containing centromere positions.
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
createTargetWeights: Calculate target weights
filterTargets: Remove low quality targets
filterVcfBasic: Basic VCF filter function
filterVcfMuTect: Filter VCF MuTect
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-deprecated: Deprecated functions in package 'PureCN'
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
setMappingBiasVcf: Set Mapping Bias VCF
setPriorVcf: Set Somatic Prior VCF