Man pages for HenrikBengtsson/PSCBS
Analysis of Parent-Specific DNA Copy Numbers
| AbstractCBS | The AbstractCBS class |
| as.CBS.DNAcopy | Coerces a DNAcopy object to a CBS object |
| as.data.frame.AbstractCBS | Gets the table of segments |
| as.data.frame.CBS | Gets the table of segments |
| as.DNAcopy.CBS | Coerces a CBS object to a DNAcopy object |
| bootstrapTCNandDHByRegion.PairedPSCBS | Estimate confidence intervals of TCN and DH segment levels |
| callAB.PairedPSCBS | Calls segments that are in allelic balance |
| callAllelicBalanceByDH.PairedPSCBS | Calls segments that are in allelic balance |
| callAmplifications.CBS | Calls (focal) amplifications |
| callCopyNeutralByTCNofAB.PairedPSCBS | Calls regions that are copy neutral |
| callCopyNeutral.PairedPSCBS | Calls segments that have a neutral total copy number |
| callGainsAndLosses.CBS | Calls gains and losses |
| callGNL.PairedPSCBS | Calls segments that are gained, copy neutral, or lost |
| callLOH.PairedPSCBS | Calls segments that are in LOH |
| callOutliers.CBS | Calls outliers |
| callROH.PairedPSCBS | Calls segments that are in ROH |
| callSegmentationOutliers | Calls/drops single-locus outliers along the genome |
| CBS | The CBS class |
| c.CBS | Concatenates segmentation results |
| dropChangePoints.AbstractCBS | Drops zero or more change points |
| dropRegions.AbstractCBS | Drops chromosomal regions (a connected set of segments) |
| estimateDeltaABBySmallDH.PairedPSCBS | Estimate a threshold for calling allelic balance from DH |
| estimateDeltaAB.PairedPSCBS | Estimate a threshold for calling allelic balance from DH |
| estimateDeltaCN.PairedPSCBS | Estimates the length of one total copy-number (TCN) unit |
| estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS | Estimate a threshold for calling LOH from DH |
| estimateDeltaLOH.PairedPSCBS | Estimate a threshold for calling LOH from DH |
| estimateKappaByC1Density.PairedPSCBS | Estimate global background in segmented copy numbers |
| estimateKappa.PairedPSCBS | Estimate global background in segmented copy numbers |
| estimateStandardDeviation.CBS | Estimates the whole-genome standard deviation of the signals |
| exampleData | Gets an example data set |
| extractMinorMajorCNs.PairedPSCBS | Extract minor and major copy-number mean levels per segment |
| extractSegmentMeansByLocus.CBS | Extracts segments means at each locus |
| extractTCNAndDHs.PairedPSCBS | Extract TCN and DH mean levels per segment |
| findLargeGaps | Identifies gaps of a genome where there exist no observations |
| findNeutralCopyNumberState | Call segments to be copy neutral based on allelic imbalance... |
| gapsToSegments.data.frame | Gets the genomic segments that are complementary to the gaps |
| getBootstrapLocusSets.PairedPSCBS | Generates original and bootstrapped segment-specific index... |
| getCallStatistics.CBS | Calculates various call statistics per chromosome |
| getChromosomes.AbstractCBS | Gets the set of chromosomes |
| getFractionOfGenomeLost.CBS | Calculates the fraction of the genome lost, gained, or... |
| getLocusData.AbstractCBS | Gets the locus-level data |
| getSampleName.AbstractCBS | Gets the name of the sample segmented |
| getSegments.AbstractCBS | Gets the segments |
| getSegments.PSCBS | Gets the segments |
| getSmoothLocusData.CBS | Gets smoothed locus-level data |
| hclustCNs.AbstractCBS | Performs a hierarchical clustering of the CN mean levels |
| installDNAcopy | Install the DNAcopy package |
| joinSegments.CBS | Joins neighboring segments such that there is no gap in... |
| mergeNonCalledSegments.CBS | Merge neighboring segments that are not called |
| mergeThreeSegments.AbstractCBS | Merge a segment and its two flanking segments |
| mergeTwoSegments.AbstractCBS | Merge two neighboring segments |
| mergeTwoSegments.PairedPSCBS | Merge two neighboring segments |
| nbrOfChangePoints.AbstractCBS | Gets the number of change points |
| nbrOfChromosomes.AbstractCBS | Gets the number of chromosomes |
| nbrOfLoci.AbstractCBS | Gets the number of loci |
| nbrOfSegments.AbstractCBS | Gets the number of segments |
| Non-documented_objects | Non-documented objects |
| NonPairedPSCBS | The NonPairedPSCBS class |
| normalizeTotalCNs.AbstractCBS | Normalizes copy numbers such that the whole-genome average... |
| PairedPSCBS | The PairedPSCBS class |
| ploidy.AbstractCBS | Gets and sets ploidy |
| plotTracks1.PairedPSCBS | Plots parental specific copy numbers along the genome |
| plotTracks.AbstractCBS | Plots the segmentation result along the genome |
| plotTracks.CBS | Plots copy numbers along the genome |
| pruneByDP.AbstractCBS | Prunes the CN profile using dynamical programming |
| pruneByHClust.AbstractCBS | Prunes the CN profile by pruning and merging through... |
| pruneBySdUndo.CBS | Prune the CBS profile by dropping change points that are too... |
| PSCBS | The PSCBS class |
| PSCBS-package | Package PSCBS |
| randomSeed | Sets and resets the .Random.seed in the global environment |
| report.AbstractCBS | Generates a report of the segmentation results |
| resetSegments.AbstractCBS | Reset the segments |
| Restructuring_AbstractCBS_objects | Restructuring AbstractCBS objects |
| segmentByCBS | Segment genomic signals using the CBS method |
| segmentByNonPairedPSCBS | Segment total copy numbers and allele B fractions using the... |
| segmentByPairedPSCBS | Segment total copy numbers and allele B fractions using the... |
| setSampleName.AbstractCBS | Sets the name of the sample segmented |
| testROH.numeric | Tests if a segment is in Run-of-Homozygosity (ROH) |
| updateMeans.AbstractCBS | Updates the CN mean levels for each segment independently |
| updateMeansTogether.AbstractCBS | Updates the CN mean levels jointly in sets of segments |
| weightedQuantile | Weighted Quantile Value |
| writeSegments.CBS | Writes the table of segments to file |
| writeSegments.PSCBS | Writes the table of segments to file |
