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PSCBS (version 0.12.2)

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

0.12.2

License

GPL (>= 2)

Maintainer

Henrik Bengtsson

Last Published

September 2nd, 2011

Functions in PSCBS (0.12.2)

PairedPSCBS

The PairedPSCBS class
estimateDeltaABBySmallDH.PairedPSCBS

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

Calls segments that are in allelic balance
Non-documented objects

Non-documented objects
estimateKappa.PairedPSCBS

Estimate global background in segmented copy numbers
segmentByPairedPSCBS

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

Plots parental specific copy numbers along the genome
segmentByCBS

Segment genomic signals using the CBS method
estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS

Estimate a threshold for calling LOH from DH
installDNAcopy

Install the DNAcopy package
plotTracks.CBS

Plots copy numbers along the genome
estimateDeltaLOH.PairedPSCBS

Estimate a threshold for calling LOH from DH
callAB.PairedPSCBS

Calls segments that are in allelic balance
estimateDeltaAB.PairedPSCBS

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

Calls segments that are in LOH
PSCBS-package

Package PSCBS
estimateKappaByC1Density.PairedPSCBS

Estimate global background in segmented copy numbers
as.data.frame.PairedPSCBS

Gets the table of segments
callSegmentationOutliers

Calls single-locus outliers along the genome
weightedQuantile

Weighted Quantile Value