segClass-class: Class "segClass"

In segmentSeq: Methods for identifying small RNA loci from high-throughput sequencing data

Description

The segClass class contains data about potential segments on the genome.

Objects from the class

Objects can be created by calls of the form new("segClass", ..., seglens). However, more usually they will be created by calling the processAD function.

Slots

coordinates:

A GRanges object defining the coordinates of the segments.

replicates:

Object of class "factor". The replicate structure for the samples.

locLikelihoods:

Object of class "DataFrame" describing estimated likelihoods that each region defined in ‘coordinates’ is a locus in each replicate group.

Details

The @coordinates slot contains information on each of the potential segments; specifically, chromosome, start and end of the segment, together. Each row of the @coordinates slot should correspond to the same row of the @data slot.

In almost all cases objects of this class should be produced by the processAD function.

Methods

Methods 'new', 'dim', '[' and 'show' have been defined for this class.

Author(s)

Thomas J. Hardcastle

See Also

processAD, the function that will most often be used to create objects of this class. segData, which inherits from this class. segMeth, which inherits from this class.

segmentSeq documentation built on Nov. 8, 2020, 5:18 p.m.