MTuples-class: An S4 class to represent m-tuples of genomic positions.

In PeteHaitch/cometh: Analyse, manage and visualise co-methylation data.

Description

An S4 class to represent m-tuples of genomic positions.

Details

The MTuples class extends the GRanges class by adding the extraPos slot (see below for details). An m-tuple is a tuple of individual basepairs that are on the same chromosome, where 'm' is the number of positions in the tuple. For example, (chr1:30, chr1:33, chr1:40) is a 3-tuple of the positions on chromosome 1. Note the strand of the m-tuple is optional.

Internally, this example 3-tuple is stored as a GRanges object with the first and last positions of the m-tuple stored as the start and end of the GRanges interval, respectively. That is, GRanges('chr1', IRanges(start = 30, end = 40)). The "extra" position, chr1:33, is stored in the extraPos matrix.

Slots

extraPos

A numeric matrix storing "extra" positions in m-tuples, provided m >= 3. If m = 1 or 2, extraPos is a matrix of NA. The extraPos matrix has as many rows as there are m-tuples in the MTuples object.

Constructor

TODO: Insert help for constructor method.

Coercion

TODO: Insert help for any coerction methods.

Accessors

TODO: Insert help for any accessor methods.

Splitting and combining

TODO: Insert help for any splitting and combining methods.

Subsetting

TODO: Describe any subsetting methods.

Filtering

TODO: Describe any filtering methods.

Methods based on findOverlaps

TODO Insert help for any findOverlaps-based methods.

Other methods

TODO: Describe any other methods.

PeteHaitch/cometh documentation built on May 8, 2019, 1:32 a.m.