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PSCBS (version 0.15.4)

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

0.15.4

License

GPL (>= 2)

Maintainer

Henrik Bengtsson

Last Published

November 2nd, 2011

Functions in PSCBS (0.15.4)

as.CBS.DNAcopy

Coerces a DNAcopy object to a CBS object

estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS

Estimate a threshold for calling LOH from DH

as.data.frame.AbstractCBS

Gets the table of segments

append.CBS

Appends one segmentation result to another

PairedPSCBS

The PairedPSCBS class

load.AbstractCBS

Loads an AbstractCBS object from file

nbrOfLoci.AbstractCBS

Gets the number of loci

extractMinorMajorCNs.PairedPSCBS

Extract minor and major copy-number mean levels per segment

extractTCNAndDHs.PairedPSCBS

Extract TCN and DH mean levels per segment

installDNAcopy

Install the DNAcopy package

dropRegions.AbstractCBS

Drops chromosomal regions (a connected set of segments)

estimateDeltaABBySmallDH.PairedPSCBS

Estimate a threshold for calling allelic balance from DH

segmentByCBS

Segment genomic signals using the CBS method

PSCBS

The PSCBS class

callGainsAndLosses.CBS

Calls gains and losses

Non-documented objects

mergeNonCalledSegments.CBS

Merge neighboring segments that are not called

getChromosomes.AbstractCBS

Gets the set of chromosomes

getSampleName.AbstractCBS

Gets the name of the sample segmented

plotTracks.AbstractCBS

Plots the segmentation result along the genome

callLOH.PairedPSCBS

Calls segments that are in LOH

extractSegmentMeansByLocus.CBS

Extracts segments means at each locus

nbrOfChangePoints.AbstractCBS

Gets the number of change points

estimateKappaByC1Density.PairedPSCBS

Estimate global background in segmented copy numbers

save.AbstractCBS

Saves an AbstractCBS object to file

plotTracks.CBS

Plots copy numbers along the genome

writeSegments.CBS

Writes the table of segments to file

AbstractCBS

The AbstractCBS class

mergeThreeSegments.AbstractCBS

Merge a segment and its two flanking segments

setSampleName.AbstractCBS

Sets the name of the sample segmented

CBS

The CBS class

as.data.frame.CBS

Gets the table of segments

getSegments.AbstractCBS

Gets the segments

getFractionOfGenomeLost.CBS

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

mergeTwoSegments.AbstractCBS

Merge two neighboring segments

nbrOfSegments.AbstractCBS

Gets the number of segments

append.PSCBS

Appends one segmentation result to another

as.DNAcopy.CBS

Coerces a CBS object to a DNAcopy object

weightedQuantile

Weighted Quantile Value

callSegmentationOutliers

Calls single-locus outliers along the genome

PSCBS-package

Package PSCBS

append.AbstractCBS

Appends one segmentation result to another

callAB.PairedPSCBS

Calls segments that are in allelic balance

getCallStatistics.CBS

Calculates various call statistics per chromosome

getLocusData.AbstractCBS

Gets the locus-level data

getSegments.PSCBS

Gets the segments

estimateDeltaLOH.PairedPSCBS

Estimate a threshold for calling LOH from DH

nbrOfChromosomes.AbstractCBS

Gets the number of chromosomes

estimateStandardDeviation.CBS

Estimates the whole-genome standard deviation of the signals

plotTracks.PairedPSCBS

Plots parental specific copy numbers along the genome

callOutliers.CBS

Calls outliers

segmentByPairedPSCBS

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

estimateDeltaAB.PairedPSCBS

Estimate a threshold for calling allelic balance from DH

callAllelicBalanceByDH.PairedPSCBS

Calls segments that are in allelic balance

callAmplifications.CBS

Calls (focal) amplifications

Restructuring AbstractCBS objects

estimateKappa.PairedPSCBS

Estimate global background in segmented copy numbers

mergeTwoSegments.PairedPSCBS

Merge two neighboring segments