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PSCBS (version 0.16.0)

Analysis of Parent-Specific DNA Copy Numbers

Description

Segments allele-specific DNA copy number data to detect regions with abnormal copy number within each parental chromosome

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Version

Install

install.packages('PSCBS')

Monthly Downloads

793

Version

0.16.0

License

GPL (>= 2)

Maintainer

Henrik Bengtsson

Last Published

November 14th, 2011

Functions in PSCBS (0.16.0)

callOutliers.CBS

Calls outliers

append.CBS

Appends one segmentation result to another

dropRegions.AbstractCBS

Drops chromosomal regions (a connected set of segments)

writeSegments.CBS

Writes the table of segments to file

PSCBS

The PSCBS class

setSampleName.AbstractCBS

Sets the name of the sample segmented

mergeTwoSegments.PairedPSCBS

Merge two neighboring segments

PSCBS-package

Package PSCBS

getSegments.AbstractCBS

Gets the segments

nbrOfLoci.AbstractCBS

Gets the number of loci

getSegments.PSCBS

Gets the segments

AbstractCBS

The AbstractCBS class

extractTCNAndDHs.PairedPSCBS

Extract TCN and DH mean levels per segment

nbrOfSegments.AbstractCBS

Gets the number of segments

PairedPSCBS

The PairedPSCBS class

nbrOfChangePoints.AbstractCBS

Gets the number of change points

segmentByPairedPSCBS

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

estimateKappaByC1Density.PairedPSCBS

Estimate global background in segmented copy numbers

callAllelicBalanceByDH.PairedPSCBS

Calls segments that are in allelic balance

estimateDeltaABBySmallDH.PairedPSCBS

Estimate a threshold for calling allelic balance from DH

callLOH.PairedPSCBS

Calls segments that are in LOH

weightedQuantile

Weighted Quantile Value

append.AbstractCBS

Appends one segmentation result to another

as.DNAcopy.CBS

Coerces a CBS object to a DNAcopy object

CBS

The CBS class

append.PSCBS

Appends one segmentation result to another

callAmplifications.CBS

Calls (focal) amplifications

load.AbstractCBS

Loads an AbstractCBS object from file

Restructuring AbstractCBS objects

estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS

Estimate a threshold for calling LOH from DH

getLocusData.AbstractCBS

Gets the locus-level data

as.data.frame.AbstractCBS

Gets the table of segments

mergeThreeSegments.AbstractCBS

Merge a segment and its two flanking segments

estimateStandardDeviation.CBS

Estimates the whole-genome standard deviation of the signals

mergeNonCalledSegments.CBS

Merge neighboring segments that are not called

Non-documented objects

as.data.frame.CBS

Gets the table of segments

estimateDeltaLOH.PairedPSCBS

Estimate a threshold for calling LOH from DH

estimateDeltaAB.PairedPSCBS

Estimate a threshold for calling allelic balance from DH

extractMinorMajorCNs.PairedPSCBS

Extract minor and major copy-number mean levels per segment

callGainsAndLosses.CBS

Calls gains and losses

as.CBS.DNAcopy

Coerces a DNAcopy object to a CBS object

getFractionOfGenomeLost.CBS

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

nbrOfChromosomes.AbstractCBS

Gets the number of chromosomes

callSegmentationOutliers

Calls single-locus outliers along the genome

getSampleName.AbstractCBS

Gets the name of the sample segmented

installDNAcopy

Install the DNAcopy package

estimateKappa.PairedPSCBS

Estimate global background in segmented copy numbers

plotTracks.PairedPSCBS

Plots parental specific copy numbers along the genome

extractSegmentMeansByLocus.CBS

Extracts segments means at each locus

getCallStatistics.CBS

Calculates various call statistics per chromosome

callAB.PairedPSCBS

Calls segments that are in allelic balance

callROH.PairedPSCBS

Calls segments that are in ROH

segmentByCBS

Segment genomic signals using the CBS method

getChromosomes.AbstractCBS

Gets the set of chromosomes

plotTracks.AbstractCBS

Plots the segmentation result along the genome

mergeTwoSegments.AbstractCBS

Merge two neighboring segments

plotTracks.CBS

Plots copy numbers along the genome

save.AbstractCBS

Saves an AbstractCBS object to file