CNVDetectionResult-class {cn.mops} | R Documentation

## Class "CNVDetectionResult"

### 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

    showClass("CNVDetectionResult")

[Package cn.mops version 1.26.0 Index]