CNSet-class {oligoClasses} | R Documentation

## Class "CNSet"

### Description

CNSet is a container for intermediate data and parameters pertaining to allele-specific copy number estimation. Methods for CNSet objects, including accessors for linear model parameters and allele-specific copy number are included here.

### Objects from the Class

An object from the class is not generally intended to be initialized by the user, but returned by the `genotype` function in the `crlmm` package.

The following creates a very basic `CNSet` with `assayData` containing the required elements.

`new(CNSet, alleleA=new("matrix"), alleleB=new("matrix"), call=new("matrix"), callProbability=new("matrix"), batch=new("factor"))`

### Slots

`batch`:

  Object of class `"factor"` ~~

`batchStatistics`:

  Object of class `"AssayData"` ~~

`assayData`:

  Object of class `"AssayData"` ~~

`phenoData`:

  Object of class `"AnnotatedDataFrame"` ~~

`featureData`:

  Object of class `"AnnotatedDataFrame"` ~~

`experimentData`:

  Object of class `"MIAME"` ~~

`annotation`:

  Object of class `"character"` ~~

`protocolData`:

  Object of class `"AnnotatedDataFrame"` ~~

`datadir`:

  Object of class `"list"`~~

`mixtureParams`:

  Object of class `"matrix"`~~

`.__classVersion__`:

  Object of class `"Versions"` ~~

### Methods

The argument `object` for the following methods is a `CNSet`.

  `object[i, j]`: subset the `CNSet` object by markers (i) and/or samples (j).

  `A(objet)`: accessor for the normalized intensities of allele A

  `A(object) <- value`: replace intensities for the A allele intensities by `value`. The object `value` must be a `matrix`, `ff_matrix`, or `ffdf`.

  `allele(object, allele)`: accessor for the normalized intensities for the A or B allele. The argument for `allele` must be either 'A' or 'B'

  `B(objet)`: accessor for the normalized intensities of allele B

  `B(object) <- value`: replace intensities for the B allele intensities by `value`. The object `value` must be a `matrix`, `ff_matrix`, or `ffdf`.

  `batch(object)`: vector of batch labels for each sample.

  `batchNames(object)`: the unique batch names

  `batchNames(object) <- value`: relabel the batches

  `calls(object)`: accessor for genotype calls coded as 1 (AA), 2 (AB), or 3 (BB). Nonpolymorphic markers are `NA`.

  `confs(object)`: accessor for the genotype confidence scores.

  `close(object)`: close any open file connections to `ff` objects stored in the `CNSet` object.

  `as(object, "oligoSnpSet")`: coerce a `CNSet` object to an object of class `oligoSnpSet` – a container for the total copy number and genotype calls.

  `corr(object)`: the correlation of the A and B intensities within each genotype.

  `flags(object)`: flags to indicate possible problems with the copy number estimation. Not fully implemented at this point.

  `new("CNSet")`: instantiating a `CNSet` object.

  `nu(object, allele)`: accessor for the intercept (background) for the A and B alleles. The value of `allele` must be 'A' or 'B'.

  `open(object)` open file connections for all `ff` objects stored in the `CNSet` object.

  `nu(object, allele)`: accessor for the slope for the A and B alleles. The value of `allele` must be 'A' or 'B'.

  `sigma2(object, allele)`: accessor for the within genotype variance

  `tau2(object, allele)`: accessor for background variance

### Author(s)

R. Scharpf

### Examples

    	new("CNSet")

[Package oligoClasses version 1.56.0 Index]