BeadStudioSetList-class: List classes with assay data listed by chromosome

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

Description

Container for log R ratios and B allele frequencies stored by chromosome.

Slots

assayDataList:

Object of class "AssayData" ~~

phenoData:

Object of class "AnnotatedDataFrame" ~~

featureDataList:

Object of class "list" ~~

chromosome:

Object of class "integer" ~~

annotation:

Object of class "character" ~~

genome:

Object of class "character" indicating the genome build. Valid entries are "hg18" and "hg19".

Methods defined for the class

clone2(object, id, prefix="",...)

Performs a deep copy of the ff objects in the assay data elements of object. A new object of the same class will be instantiated. The ff objects in the instantiated object will point to ff files on disk with prefix given by the argument prefix.

A use-case for such a function is that one may want to perform wave correction on the log R ratios in object, but keep a copy of the original unadjusted log R ratios. If object is not copied using clone2 prior to wave correction, the log R ratios will be updated on disk and the original, unadjusted log R ratios will no longer be available.

Accessors

baf(object)An accessor for the B allele frequencies (BAFs). The accessor returns a list where each element of the list is a matrix of the BAFs for the corresponding element in the SetList object. While the BAFs have a range [0, 1], they are often saved internally as integers by multiplying the original BAFs by 1000. Users can restore the original scale by dividing by 1000.

lrr(object) An accessor for the log R ratios, an estimate of the copy number (presumably relative to diploid copy number) at each marker on a SNP array. The accessor returns a list where each element of the list is a matrix of the log R ratios for the corresponding element in the SetList object. The log R ratios are often saved internally as integers by multiplying the original LRRs by 100 in order to reduce the memory footprint of large studies. Users can restore the original scale by dividing by 100.

Author(s)

R. Scharpf

See Also

See supporting packages for methods defined for the class.

benilton/oligoClassesOld documentation built on May 12, 2019, 11:51 a.m.