CNSet-methods {crlmm} | R Documentation

## crlmm methods for class "CNSet"

### 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`

[Package crlmm version 1.45.0 Index]