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PSCBS (version 0.38.4)

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

0.38.4

License

GPL (>= 2)

Maintainer

Henrik Bengtsson

Last Published

October 16th, 2013

Functions in PSCBS (0.38.4)

callGNL.PairedPSCBS

Calls segments that are gained, copy neutral, or lost
AbstractCBS$load

Loads an AbstractCBS object from file
append.CBS

Appends one segmentation result to another
PSCBS-package

Package PSCBS
callOutliers.CBS

Calls outliers
AbstractCBS

The AbstractCBS class
pruneByDP.AbstractCBS

Prunes the CN profile using dynamical programming
callAB.PairedPSCBS

Calls segments that are in allelic balance
hclustCNs.AbstractCBS

Performs a hierarchical clustering of the CN mean levels
getFractionOfGenomeLost.CBS

Calculates the fraction of the genome lost, gained, or aberrant either way
gapsToSegments.data.frame

Gets the genomic segments that are complementary to the gaps
as.data.frame.AbstractCBS

Gets the table of segments
NonPairedPSCBS

The NonPairedPSCBS class
estimateDeltaLOH.PairedPSCBS

Estimate a threshold for calling LOH from DH
dropChangePoints.AbstractCBS

Drops zero or more change points
callROH.PairedPSCBS

Calls segments that are in ROH
getLocusData.AbstractCBS

Gets the locus-level data
estimateKappa.PairedPSCBS

Estimate global background in segmented copy numbers
weightedQuantile

Weighted Quantile Value
segmentByNonPairedPSCBS

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

Merge two neighboring segments
callAmplifications.CBS

Calls (focal) amplifications
PSCBS

The PSCBS class
getSmoothLocusData.CBS

Gets smoothed locus-level data
estimateKappaByC1Density.PairedPSCBS

Estimate global background in segmented copy numbers
plotTracks.CBS

Plots copy numbers along the genome
updateMeansTogether.AbstractCBS

Updates the CN mean levels jointly in sets of segments
segmentByPairedPSCBS

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

Calls segments that have a neutral total copy number
updateMeans.AbstractCBS

Updates the CN mean levels for each segment independently
segmentByCBS

Segment genomic signals using the CBS method
Non-documented objects

Non-documented objects
installDNAcopy

Install the DNAcopy package
pruneBySdUndo.CBS

Prune the CBS profile by dropping change points that are too small
nbrOfChangePoints.AbstractCBS

Gets the number of change points
exampleData

Gets an example data set
nbrOfSegments.AbstractCBS

Gets the number of segments
mergeThreeSegments.AbstractCBS

Merge a segment and its two flanking segments
estimateStandardDeviation.CBS

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

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

Extracts segments means at each locus
nbrOfLoci.AbstractCBS

Gets the number of loci
append.PSCBS

Appends one segmentation result to another
dropRegions.AbstractCBS

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

Generates a report of the segmentation results
plotTracks.PairedPSCBS

Plots parental specific copy numbers along the genome
save.AbstractCBS

Saves an AbstractCBS object to file
as.data.frame.CBS

Gets the table of segments
getSegments.PSCBS

Gets the segments
writeSegments.CBS

Writes the table of segments to file
getCallStatistics.CBS

Calculates various call statistics per chromosome
callLOH.PairedPSCBS

Calls segments that are in LOH
getSampleName.AbstractCBS

Gets the name of the sample segmented
estimateDeltaABBySmallDH.PairedPSCBS

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

Gets the segments
Restructuring AbstractCBS objects

Restructuring AbstractCBS objects
resetSegments.AbstractCBS

Reset the segments
extractMinorMajorCNs.PairedPSCBS

Extract minor and major copy-number mean levels per segment
bootstrapTCNandDHByRegion.PairedPSCBS

Estimate confidence intervals of TCN and DH segment levels
getChromosomes.AbstractCBS

Gets the set of chromosomes
setSampleName.AbstractCBS

Sets the name of the sample segmented
ploidy.AbstractCBS

Gets and sets ploidy
nbrOfChromosomes.AbstractCBS

Gets the number of chromosomes
testROH.numeric

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

Plots the segmentation result along the genome
callCopyNeutralByTCNofAB.PairedPSCBS

Calls regions that are copy neutral
extractTCNAndDHs.PairedPSCBS

Extract TCN and DH mean levels per segment
pruneByHClust.AbstractCBS

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

Calls segments that are in allelic balance
as.DNAcopy.CBS

Coerces a CBS object to a DNAcopy object
CBS

The CBS class
PairedPSCBS

The PairedPSCBS class
as.CBS.DNAcopy

Coerces a DNAcopy object to a CBS object
append.AbstractCBS

Appends one segmentation result to another
callGainsAndLosses.CBS

Calls gains and losses
callSegmentationOutliers

Calls single-locus outliers along the genome
estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS

Estimate a threshold for calling LOH from DH
findNeutralCopyNumberState

Call segments to be copy neutral based on allelic imbalance calls and total copy number estimates
findLargeGaps

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

Merge neighboring segments that are not called
mergeTwoSegments.PairedPSCBS

Merge two neighboring segments
writeSegments.PSCBS

Writes the table of segments to file