R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
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Results 1 - 10 of 85 found.
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pruneByDP.AbstractCBS (Package: PSCBS) : Prunes the CN profile using dynamical programming

Prunes the CN profile using dynamical programming by specifying the target number of segments or alternative how of many change points to drop.

● Data Source: CranContrib
● Keywords: internal, methods
● Alias: AbstractCBS.pruneByDP, pruneByDP,AbstractCBS-method, pruneByDP.AbstractCBS
● 0 images

estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS (Package: PSCBS) : Estimate a threshold for calling LOH from DH

Estimate a threshold for calling LOH from DH based on the location of guessed C1=0 and C1=1 peaks.

● Data Source: CranContrib
● Keywords: internal, methods
● Alias: PairedPSCBS.estimateDeltaLOHByMinC1ForNonAB, estimateDeltaLOHByMinC1ForNonAB,PairedPSCBS-method, estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS
● 0 images

nbrOfChangePoints.AbstractCBS (Package: PSCBS) : Gets the number of change points

Gets the number of change points, which is defined as the number of segments minus the number of chromosomes.

● Data Source: CranContrib
● Keywords: internal, methods
● Alias: AbstractCBS.nbrOfChangePoints, nbrOfChangePoints,AbstractCBS-method, nbrOfChangePoints.AbstractCBS
● 0 images

append.AbstractCBS (Package: PSCBS) : Appends one segmentation result to another

Appends one segmentation result to another, where both holds segmentation results of the same sample.

● Data Source: CranContrib
● Keywords: internal, methods
● Alias: AbstractCBS.append, append,AbstractCBS-method, append.AbstractCBS
● 0 images

segmentByNonPairedPSCBS (Package: PSCBS) : Segment total copy numbers and allele B fractions using the Non-paired PSCBS method

Segment total copy numbers and allele B fractions using the Non-paired PSCBS method [1]. This method does not requires matched normals. This is a low-level segmentation method. It is intended to be applied to one tumor sample at the time.

● Data Source: CranContrib
● Keywords: IO
● Alias: segmentByNonPairedPSCBS, segmentByNonPairedPSCBS.PairedPSCBS, segmentByNonPairedPSCBS.data.frame, segmentByNonPairedPSCBS.default
● 1 images

callROH.PairedPSCBS (Package: PSCBS) : Calls segments that are in ROH

Calls segments that are in ROH, i.e. that have no (true) heterozygous genotypes. Run of homozygosity (ROH) is a property of the normal (germline) sample.

● Data Source: CranContrib
● Keywords: internal, methods
● Alias: PairedPSCBS.callROH, callROH,PairedPSCBS-method, callROH.NonPairedPSCBS, callROH.PairedPSCBS
● 0 images

testROH.numeric (Package: PSCBS) : Tests if a segment is in Run-of-Homozygosity (ROH)

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

● Data Source: CranContrib
● Keywords: internal, methods
● Alias: testROH.numeric
● 0 images

append.CBS (Package: PSCBS) : Appends one segmentation result to another

Appends one segmentation result to another.

● Data Source: CranContrib
● Keywords: internal, methods
● Alias: CBS.append, append,CBS-method, append.CBS
● 0 images

pruneBySdUndo.CBS (Package: PSCBS) : Prune the CBS profile by dropping change points that are too small

Prune the CBS profile by dropping change points that are too small, where "too small" means that the amplitude of the change points is less than a multiple of the overall standard deviation of the copy-number signals.

● Data Source: CranContrib
● Keywords: internal, methods
● Alias: CBS.pruneBySdUndo, pruneBySdUndo,CBS-method, pruneBySdUndo.CBS
● 1 images

AbstractCBS (Package: PSCBS) : The AbstractCBS class

Package: PSCBS
Class AbstractCBS

● Data Source: CranContrib
● Keywords: classes, internal
● Alias: AbstractCBS
● 0 images