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PSCBS (version 0.63.0)

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

0.63.0

License

GPL (>= 2)

Issues

10

Pull Requests

1

Stars

7

Forks

4

Maintainer

Henrik Bengtsson

Last Published

June 28th, 2017

Functions in PSCBS (0.63.0)

Non-documented objects

Non-documented objects
NonPairedPSCBS

The NonPairedPSCBS class
PSCBS-package

Package PSCBS
PairedPSCBS

The PairedPSCBS class
Restructuring AbstractCBS objects

Restructuring AbstractCBS objects
append.AbstractCBS

Appends one segmentation result to another
append.CBS

Appends one segmentation result to another
AbstractCBS

The AbstractCBS class
CBS

The CBS class
PSCBS

The PSCBS class
as.DNAcopy.CBS

Coerces a CBS object to a DNAcopy object
as.data.frame.AbstractCBS

Gets the table of segments
callGainsAndLosses.CBS

Calls gains and losses
callAB.PairedPSCBS

Calls segments that are in allelic balance
callAllelicBalanceByDH.PairedPSCBS

Calls segments that are in allelic balance
callOutliers.CBS

Calls outliers
callROH.PairedPSCBS

Calls segments that are in ROH
callLOH.PairedPSCBS

Calls segments that are in LOH
estimateStandardDeviation.CBS

Estimates the whole-genome standard deviation of the signals
exampleData

Gets an example data set
getBootstrapLocusSets.PairedPSCBS

Generates original and bootstrapped segment-specific index sets
append.PSCBS

Appends one segmentation result to another
as.CBS.DNAcopy

Coerces a DNAcopy object to a CBS object
dropRegions.AbstractCBS

Drops chromosomal regions (a connected set of segments)
estimateDeltaAB.PairedPSCBS

Estimate a threshold for calling allelic balance from DH
estimateKappa.PairedPSCBS

Estimate global background in segmented copy numbers
estimateKappaByC1Density.PairedPSCBS

Estimate global background in segmented copy numbers
extractTCNAndDHs.PairedPSCBS

Extract TCN and DH mean levels per segment
findLargeGaps

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

Calculates various call statistics per chromosome
getSmoothLocusData.CBS

Gets smoothed locus-level data
hclustCNs.AbstractCBS

Performs a hierarchical clustering of the CN mean levels
as.data.frame.CBS

Gets the table of segments
bootstrapTCNandDHByRegion.PairedPSCBS

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

Calls regions that are copy neutral
callGNL.PairedPSCBS

Calls segments that are gained, copy neutral, or lost
installDNAcopy

Install the DNAcopy package
joinSegments.CBS

Joins neighboring segments such that there is no gap in between them
ploidy.AbstractCBS

Gets and sets ploidy
plotTracks.AbstractCBS

Plots the segmentation result along the genome
segmentByNonPairedPSCBS

Segment total copy numbers and allele B fractions using the Non-paired PSCBS method
segmentByPairedPSCBS

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

Extract minor and major copy-number mean levels per segment
extractSegmentMeansByLocus.CBS

Extracts segments means at each locus
getChromosomes.AbstractCBS

Gets the set of chromosomes
getFractionOfGenomeLost.CBS

Calculates the fraction of the genome lost, gained, or aberrant either way
AbstractCBS$load

Loads an AbstractCBS object from file
mergeNonCalledSegments.CBS

Merge neighboring segments that are not called
nbrOfChromosomes.AbstractCBS

Gets the number of chromosomes
nbrOfLoci.AbstractCBS

Gets the number of loci
pruneBySdUndo.CBS

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

Estimate a threshold for calling LOH from DH
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
gapsToSegments.data.frame

Gets the genomic segments that are complementary to the gaps
randomSeed

Sets and resets the .Random.seed in the global environment
updateMeans.AbstractCBS

Updates the CN mean levels for each segment independently
updateMeansTogether.AbstractCBS

Updates the CN mean levels jointly in sets of segments
getSegments.AbstractCBS

Gets the segments
getSegments.PSCBS

Gets the segments
plotTracks.CBS

Plots copy numbers along the genome
plotTracks.PairedPSCBS

Plots parental specific 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 hierarchical clustering
setSampleName.AbstractCBS

Sets the name of the sample segmented
nbrOfSegments.AbstractCBS

Gets the number of segments
normalizeTotalCNs.AbstractCBS

Normalizes copy numbers such that the whole-genome average total copy number is two
save.AbstractCBS

Saves an AbstractCBS object to file
segmentByCBS

Segment genomic signals using the CBS method
writeSegments.PSCBS

Writes the table of segments to file
testROH.numeric

Tests if a segment is in Run-of-Homozygosity (ROH)
callAmplifications.CBS

Calls (focal) amplifications
callCopyNeutral.PairedPSCBS

Calls segments that have a neutral total copy number
callSegmentationOutliers

Calls/drops single-locus outliers along the genome
dropChangePoints.AbstractCBS

Drops zero or more change points
estimateDeltaABBySmallDH.PairedPSCBS

Estimate a threshold for calling allelic balance from DH
estimateDeltaCN.PairedPSCBS

Estimates the length of one total copy-number (TCN) unit
getLocusData.AbstractCBS

Gets the locus-level data
getSampleName.AbstractCBS

Gets the name of the sample segmented
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
report.AbstractCBS

Generates a report of the segmentation results
resetSegments.AbstractCBS

Reset the segments
weightedQuantile

Weighted Quantile Value
writeSegments.CBS

Writes the table of segments to file