oligoSnpSet-methods {oligoClasses} | R Documentation

## Methods for oligoSnpSet class

### Description

Methods for oligoSnpSet class

### Methods

In the following code, `object` is an instance of the `oligoSnpSet` class.

  `new("oligoSnpSet", ...)`: Instantiates an object of class `oligoSnpSet`. The assayData elements of the `oligoSnpSet` class can include matrices of genotype calls, confidence scores for the genotype calls, B allele frequencies, absolute or relative copy number, and confidence scores for the copy number estimates. Each matrix should be coerced to an integer scale prior to assignment to the `oligoSnpSet` object. Validity methods defined for the class will fail if the matrices are not integers. See examples for additional details.

  `baf(object)`: Accessor for integer representation of the B allele frequencies. The value returned by this method can be divided by 1000 to obtain B allele frequencies on the original [0,1] scale.

  `baf(object) <- value`: Assign an integer representation of the B allele frequencies to the 'baf' element of the assayData slot. `value` must be a matrix of integers. See the examples for help converting BAFs to a matrix of integers.

[Package oligoClasses version 1.42.0 Index]