segData-class {segmentSeq} | R Documentation

## Class "segData"

### 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)

[Package segmentSeq version 2.28.0 Index]