Methods for oligoSnpSet class
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.
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