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PSCBS (version 0.35.6)

Analysis of Parent-Specific DNA Copy Numbers

Description

Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

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Version

Install

install.packages('PSCBS')

Monthly Downloads

793

Version

0.35.6

License

GPL (>= 2)

Maintainer

Henrik Bengtsson

Last Published

August 2nd, 2013

Functions in PSCBS (0.35.6)

bootstrapTCNandDHByRegion.PairedPSCBS

Estimate confidence intervals of TCN and DH segment levels
callCopyNeutralByTCNofAB.PairedPSCBS

Calls regions that are copy neutral
as.DNAcopy.CBS

Coerces a CBS object to a DNAcopy object
Non-documented objects

Non-documented objects
as.data.frame.AbstractCBS

Gets the table of segments
getSegments.AbstractCBS

Gets the segments
as.data.frame.CBS

Gets the table of segments
PSCBS

The PSCBS class
callCopyNeutral.PairedPSCBS

Calls segments that have a neutral total copy number
estimateStandardDeviation.CBS

Estimates the whole-genome standard deviation of the signals
callLOH.PairedPSCBS

Calls segments that are in LOH
extractMinorMajorCNs.PairedPSCBS

Extract minor and major copy-number mean levels per segment
segmentByCBS

Segment genomic signals using the CBS method
gapsToSegments.data.frame

Gets the genomic segments that are complementary to the gaps
extractSegmentMeansByLocus.CBS

Extracts segments means at each locus
Restructuring AbstractCBS objects

Restructuring AbstractCBS objects
NonPairedPSCBS

The NonPairedPSCBS class
as.CBS.DNAcopy

Coerces a DNAcopy object to a CBS object
extractTCNAndDHs.PairedPSCBS

Extract TCN and DH mean levels per segment
getFractionOfGenomeLost.CBS

Calculates the fraction of the genome lost, gained, or aberrant either way
pruneByHClust.AbstractCBS

Prunes the CN profile by pruning and merging through hierarchical clustering
estimateKappaByC1Density.PairedPSCBS

Estimate global background in segmented copy numbers
segmentByPairedPSCBS

Segment total copy numbers and allele B fractions using the Paired PSCBS method
plotTracks.PairedPSCBS

Plots parental specific copy numbers along the genome
getSampleName.AbstractCBS

Gets the name of the sample segmented
pruneByDP.AbstractCBS

Prunes the CN profile using dynamical programming
installDNAcopy

Install the DNAcopy package
save.AbstractCBS

Saves an AbstractCBS object to file
append.AbstractCBS

Appends one segmentation result to another
plotTracks.CBS

Plots copy numbers along the genome
estimateDeltaAB.PairedPSCBS

Estimate a threshold for calling allelic balance from DH
report.AbstractCBS

Generates a report of the segmentation results
getSmoothLocusData.CBS

Gets smoothed locus-level data
append.CBS

Appends one segmentation result to another
testROH.numeric

Tests if a segment is in Run-of-Homozygosity (ROH)
plotTracks.AbstractCBS

Plots the segmentation result along the genome
findNeutralCopyNumberState

Call segments to be copy neutral based on allelic imbalance calls and total copy number estimates
append.PSCBS

Appends one segmentation result to another
getChromosomes.AbstractCBS

Gets the set of chromosomes
callROH.PairedPSCBS

Calls segments that are in ROH
writeSegments.CBS

Writes the table of segments to file
callGNL.PairedPSCBS

Calls segments that are gained, copy neutral, or lost
mergeThreeSegments.AbstractCBS

Merge a segment and its two flanking segments
setSampleName.AbstractCBS

Sets the name of the sample segmented
resetSegments.AbstractCBS

Reset the segments
exampleData

Gets an example data set
AbstractCBS

The AbstractCBS class
dropRegions.AbstractCBS

Drops chromosomal regions (a connected set of segments)
getLocusData.AbstractCBS

Gets the locus-level data
mergeTwoSegments.PairedPSCBS

Merge two neighboring segments
estimateDeltaLOH.PairedPSCBS

Estimate a threshold for calling LOH from DH
nbrOfChromosomes.AbstractCBS

Gets the number of chromosomes
writeSegments.PSCBS

Writes the table of segments to file
updateMeansTogether.AbstractCBS

Updates the CN mean levels jointly in sets of segments
weightedQuantile

Weighted Quantile Value
hclustCNs.AbstractCBS

Performs a hierarchical clustering of the CN mean levels
getSegments.PSCBS

Gets the segments
PairedPSCBS

The PairedPSCBS class
callAmplifications.CBS

Calls (focal) amplifications
callOutliers.CBS

Calls outliers
callSegmentationOutliers

Calls single-locus outliers along the genome
estimateDeltaABBySmallDH.PairedPSCBS

Estimate a threshold for calling allelic balance from DH
mergeNonCalledSegments.CBS

Merge neighboring segments that are not called
nbrOfLoci.AbstractCBS

Gets the number of loci
estimateKappa.PairedPSCBS

Estimate global background in segmented copy numbers
AbstractCBS$load

Loads an AbstractCBS object from file
CBS

The CBS class
callAllelicBalanceByDH.PairedPSCBS

Calls segments that are in allelic balance
callGainsAndLosses.CBS

Calls gains and losses
nbrOfSegments.AbstractCBS

Gets the number of segments
mergeTwoSegments.AbstractCBS

Merge two neighboring segments
nbrOfChangePoints.AbstractCBS

Gets the number of change points
PSCBS-package

Package PSCBS
segmentByNonPairedPSCBS

Segment total copy numbers and allele B fractions using the Non-paired PSCBS method
pruneBySdUndo.CBS

Prune the CBS profile by dropping change points that are too small
callAB.PairedPSCBS

Calls segments that are in allelic balance
dropChangePoints.AbstractCBS

Drops zero or more change points
estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS

Estimate a threshold for calling LOH from DH
findLargeGaps

Identifies gaps of a genome where there exist no observations
getCallStatistics.CBS

Calculates various call statistics per chromosome
ploidy.AbstractCBS

Gets and sets ploidy
updateMeans.AbstractCBS

Updates the CN mean levels for each segment independently