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PSCBS (version 0.23.0)

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

0.23.0

License

GPL (>= 2)

Maintainer

Henrik Bengtsson

Last Published

March 21st, 2012

Functions in PSCBS (0.23.0)

save.AbstractCBS

Saves an AbstractCBS object to file

Non-documented objects

callGainsAndLosses.CBS

Calls gains and losses

callSegmentationOutliers

Calls single-locus outliers along the genome

as.data.frame.CBS

Gets the table of segments

findNeutralCopyNumberState

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

PairedPSCBS

The PairedPSCBS class

Restructuring AbstractCBS objects

writeSegments.CBS

Writes the table of segments to file

mergeTwoSegments.AbstractCBS

Merge two neighboring segments

dropChangePoints.AbstractCBS

Drops zero or more change points

mergeTwoSegments.PairedPSCBS

Merge two neighboring segments

getFractionOfGenomeLost.CBS

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

PSCBS

The PSCBS class

installDNAcopy

Install the DNAcopy package

nbrOfSegments.AbstractCBS

Gets the number of segments

nbrOfLoci.AbstractCBS

Gets the number of loci

estimateStandardDeviation.CBS

Estimates the whole-genome standard deviation of the signals

findLargeGaps

Identifies gaps of a genome where there exist no observations

extractTCNAndDHs.PairedPSCBS

Extract TCN and DH mean levels per segment

append.PSCBS

Appends one segmentation result to another

segmentByCBS

Segment genomic signals using the CBS method

as.DNAcopy.CBS

Coerces a CBS object to a DNAcopy object

estimateKappa.PairedPSCBS

Estimate global background in segmented copy numbers

callGNL.PairedPSCBS

Calls segments that are gained, copy neutral, or lost

getSegments.PSCBS

Gets the segments

extractSegmentMeansByLocus.CBS

Extracts segments means at each locus

setSampleName.AbstractCBS

Sets the name of the sample segmented

AbstractCBS

The AbstractCBS class

callAmplifications.CBS

Calls (focal) amplifications

estimateDeltaABBySmallDH.PairedPSCBS

Estimate a threshold for calling allelic balance from DH

pruneByHClust.AbstractCBS

Prunes the CN profile by pruning and merging through hierarchical clustering

dropRegions.AbstractCBS

Drops chromosomal regions (a connected set of segments)

plotTracks.AbstractCBS

Plots the segmentation result along the genome

callAllelicBalanceByDH.PairedPSCBS

Calls segments that are in allelic balance

hclustCNs.AbstractCBS

Performs a hierarchical clustering of the CN mean levels

extractMinorMajorCNs.PairedPSCBS

Extract minor and major copy-number mean levels per segment

getSampleName.AbstractCBS

Gets the name of the sample segmented

updateMeansTogether.AbstractCBS

Updates the CN mean levels jointly in sets of segments

writeSegments.PSCBS

Writes the table of segments to file

report.PairedPSCBS

Generates a report of the Paired PSCBS results

callCN.PairedPSCBS

Calls segments that are copy neutral

nbrOfChromosomes.AbstractCBS

Gets the number of chromosomes

estimateKappaByC1Density.PairedPSCBS

Estimate global background in segmented copy numbers

getSegments.AbstractCBS

Gets the segments

append.CBS

Appends one segmentation result to another

CBS

The CBS class

estimateDeltaAB.PairedPSCBS

Estimate a threshold for calling allelic balance from DH

load.AbstractCBS

Loads an AbstractCBS object from file

callLOH.PairedPSCBS

Calls segments that are in LOH

as.data.frame.AbstractCBS

Gets the table of segments

getLocusData.AbstractCBS

Gets the locus-level data

append.AbstractCBS

Appends one segmentation result to another

callROH.PairedPSCBS

Calls segments that are in ROH

estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS

Estimate a threshold for calling LOH from DH

gapsToSegments.data.frame

Gets the genomic segments that are complementary to the gaps

weightedQuantile

Weighted Quantile Value

callCopyNeutralByTCNofAB.PairedPSCBS

Calls regions that are copy neutral

callAB.PairedPSCBS

Calls segments that are in allelic balance

mergeNonCalledSegments.CBS

Merge neighboring segments that are not called

plotTracks.CBS

Plots copy numbers along the genome

plotTracks.PairedPSCBS

Plots parental specific copy numbers along the genome

nbrOfChangePoints.AbstractCBS

Gets the number of change points

segmentByPairedPSCBS

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

pruneBySdUndo.CBS

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

as.CBS.DNAcopy

Coerces a DNAcopy object to a CBS object

estimateDeltaLOH.PairedPSCBS

Estimate a threshold for calling LOH from DH

getChromosomes.AbstractCBS

Gets the set of chromosomes

getCallStatistics.CBS

Calculates various call statistics per chromosome

mergeThreeSegments.AbstractCBS

Merge a segment and its two flanking segments