alignmentData-class {segmentSeq} | R Documentation

## Class "alignmentData"

### Description

The `alignmentData` class inherits from the `alignmentClass` class and records information about a set of alignments of high-throughput sequencing data to a genome. Details include the alignments themselves, the chromosomes of the genome to which the data are aligned, and counts of the aligned tags from each of the libraries from which the data come.

### Objects from the class

Objects can be created by calls of the form `new("alignmentData", ...)`, but more usually by using one of `readBAM` or `readGeneric` functions to generate the object from a set of alignment files.

### Slots

`alignments`:

  Object of class `"GRanges"`. Stores information about the alignments. See Details.

`replicates`:

  Object of class `"factor"`. Replicate information for each of the libraries. See Details.

`data`:

  Object of class `"matrix"`. For each alignment described in the `alignments` slot, contains the number of times the alignment is seen in each sample.

`libnames`:

  Object of class `"character"`. The names of the libraries for which alignment data exists.

`libsizes`:

  Object of class `"numeric"`. The library sizes (see Details) for each of the libraries.

### Details

The `alignments` slot is the key element of this class. This is a `GRanges` object that, in addition to the usual elements defining the location of aligned objects to a reference genome, also describes the values ‘tag’, giving the sequence of the tag aligning to the location, ‘matches’, indicating in how many places that tag matches to the genome, ‘chunk’, an identifier for the sets of tags that align close enough together to form a potential locus, and ‘chunkDup’, indicating whether that tag matches to multiple places within the chunk.

The library sizes, defined in the `libsizes` slot, provide some scaling factor for the observed number of counts of a tag in different samples.

The `replicates` slot is a vector of factors such that the ith sample is a replicate of the jth sample if and only if `@replicates[i] == @replicates[j]`.

### Methods

[

  `signature(x = "alignmentData")`: ...

dim

  `signature(x = "alignmentData")`: ...

initialize

  `signature(.Object = "alignmentData")`: ...

show

  `signature(object = "alignmentData")`: ...

### Author(s)

Thomas J. Hardcastle

### See Also

`alignmentClass`, the class from which `'alignmentData'` inherits. `readGeneric`, which will produce a `'alignmentData'` object from appropriately formatted tab-delimited files. `readBAM`, which will produce a `'alignmentData'` object from BAM files. `processAD`, which will convert an `'alignmentData'` object into a 'segData' object for segmentation.

### 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)

[Package segmentSeq version 2.21.0 Index]