CNVDetectionResult: Class "CNVDetectionResult"
In cn.mops: cn.mops - Mixture of Poissons for CNV detection in NGS data
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.
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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")
|
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