Man pages for lima1/PureCN
Copy number calling and SNV classification using targeted short read sequencing
| adjustLogRatio | Adjust tumor vs. normal coverage log ratio for tumor purity... |
| annotateTargets | Annotate targets with gene symbols |
| bootstrapResults | Bootstrapping variant fits |
| calculateBamCoverageByInterval | Function to calculate coverage from BAM file |
| 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 |
| readAllelicCountsFile | Read allelic counts file |
| readCoverageFile | Read coverage file |
| readCurationFile | Read curation file |
| readIntervalFile | Read interval 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 |
| segmentationGATK4 | GATK4 ModelSegments segmentation function |
| segmentationHclust | Minimal segmentation function |
| segmentationPSCBS | PSCBS segmentation |
| setMappingBiasVcf | Set Mapping Bias VCF |
| setPriorVcf | Set Somatic Prior VCF |
