CNVDetectionResult: Class "CNVDetectionResult"

Description Slots Methods Author(s) Examples

Description

S4 class for storing results of a CNV detection method.

Slots

The following slots are defined for CNVDetectionResult objects:

gr

The segments in which the reads are counted. GRanges object.

normalizedData

The normalized data.

localAssessments

The data to which the segmentation algorithm is applied. These can be z-Scores, ratios, log-ratios or I/NI calls.

individualCall

The CNV call that the method provides for a specific sample

iniCall

The CNV call that the method provides a specific segment.

posteriorProbs

The posterior probabilities for different copy numbers.

cnvs

The detected CNVs.

cnvr

The detected CNV regions.

segmentation

The segmentation of the reference sequence (sample-wise).

integerCopyNumber

The most probable integer copy number.

sampleNames

The sample names.

params

The parameters with which the method was run.

Methods

gr

signature(object = "CNVDetectionResult"): ...

cnvr

signature(object = "CNVDetectionResult"): ...

cnvs

signature(object = "CNVDetectionResult"): ...

individualCall

signature(object = "CNVDetectionResult"): ...

iniCall

signature(object = "CNVDetectionResult"): ...

integerCopyNumber

signature(object = "CNVDetectionResult"): ...

localAssessments

signature(object = "CNVDetectionResult"): ...

normalizedData

signature(object = "CNVDetectionResult"): ...

params

signature(object = "CNVDetectionResult"): ...

plot

signature(x = "CNVDetectionResult", y = "missing"): ...

posteriorProbs

signature(object = "CNVDetectionResult"): ...

sampleNames

signature(object = "CNVDetectionResult"): ...

segmentation

signature(object = "CNVDetectionResult"): ...

segplot

signature(object = "CNVDetectionResult"): ...

show

signature(object = "CNVDetectionResult"): ...

calcIntegerCopyNumbers

signature(object = "CNVDetectionResult"): ...

makeRobustCNVR

signature(object = "CNVDetectionResult"): ...

Author(s)

Guenter Klambauer klambauer@bioinf.jku.at

Examples

1
showClass("CNVDetectionResult")

cn.mops documentation built on Nov. 8, 2020, 5:59 p.m.