oligoSnpSet-methods: Methods for oligoSnpSet class

In benilton/oligoClasses: Classes for high-throughput arrays supported by oligo and crlmm

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.

benilton/oligoClasses documentation built on Dec. 27, 2019, 12:13 a.m.