segData-class: Class "segData"

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

Description

The segData class inherits from the segClass class and contains data about potential segments on the genome, together with counts for each of those segments.

Objects from the class

Objects can be created by calls of the form new("segData", ..., 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.

data:

Object of class matrix. Contains the number of counts observed for each sample in each potential segment.

libsizes:

Object of class "numeric". The library sizes for each sample.

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. classifySeg, an empirical Bayesian method for defining a segmentation based on a segData object.

Examples

# Define the files containing sample information.

datadir <- system.file("extdata", package = "segmentSeq")
libfiles <- c("SL9.txt", "SL10.txt", "SL26.txt", "SL32.txt")

# Establish the library names and replicate structure.

libnames <- c("SL9", "SL10", "SL26", "SL32")
replicates <- c(1,1,2,2)

# Process the files to produce an 'alignmentData' object.

alignData <- readGeneric(file = libfiles, dir = datadir, replicates =
replicates, libnames = libnames)

# Process the alignmentData object to produce a 'segData' object.

sD <- processAD(alignData, gap = 100, cl = NULL)

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