alignmentClass-class {segmentSeq} | R Documentation

## Class "alignmentClass"

### Description

The `alignmentClass` class records information about a set of alignments of high-throughput sequencing data to a genome.

### Slots

`alignments`:

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

`libnames`:

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

`replicates`:

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

### Details

The `alignments` slot is a `GRanges` object defining the location of aligned objects to a reference genome.

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]`.

The `libnames` slot is a vector defining the names of the libraries described by the object.

### Methods

[

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

dim

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

initialize

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

show

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

### Author(s)

Thomas J. Hardcastle

### See Also

`alignmentData` `alignmentMeth`

[Package segmentSeq version 2.22.0 Index]