crlmm methods for class "CNSet"

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Description

CNSet is a container defined in the oligoClasses package for storing normalized intensities for genotyping platforms, genotype calls, and parameters estimated for copy number. Accessors for data that an object of this class contains are largely defined in the package oligoClasses. CNSet methods that involve more complex calculations that are specific to the crlmm package, such as computing allele-specific copy number, are included in crlmm and described here.

Methods

as(from, "oligoSnpSet"): Method for coercing object from (class CNSet) to an object of class oligoSnpSet.

CA

signature(object="CNSet"): calculates raw copy number for allele A

CB

signature(object="CNSet"): calculates raw copy number for allele B

lines

signature(x="CNSet"): plot ellipses (95th percentile) for prediction regions

totalCopynumber

signature(object="CNSet"): calculates total raw copy number

rawCopynumber

signature(object="CNSet"): same as totalCopynumber

nuA

signature(object="CNSet"): estimate of mean background (intensity-scale) for allele A

nuB

signature(object="CNSet"): estimate of mean background (intensity-scale) for allele A

phiA

signature(object="CNSet"): estimate of slope coefficient (intensity-scale) for allele A

phiB

signature(object="CNSet"): estimate of slope coefficient (intensity-scale) for allele B

Ns

signature(object="CNSet"): genotype frequencies

corr

signature(object="CNSet"): correlation of log-transformed normalized intensities within the genotype clusters

mads

signature(x="CNSet"): ...

medians

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

tau2

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

OligoSetList(object): constructs an object of class OligoSetList from object having class CNSet.

BafLrrSetList(object): constructs an object of class BafLrrSetList from object having class CNSet.

See Also

CNSet-class, CA, CB, totalCopynumber, rawCopynumber

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