alignmentMeth-class {segmentSeq} | R Documentation

## Class "alignmentMeth"

### Description

The `alignmentMeth` 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("alignmentMeth", ...)`, 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"`. Defines the location of sequenced cytosines, amongst other data. 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.

`Cs`:

  Object of class `"matrix"`. For each cytosine described in the `alignments` slot, contains the number of times the cytosine is sequenced as a 'C', and is thus methylated.

`Ts`:

  Object of class `"matrix"`. For each cytosine described in the `alignments` slot, contains the number of times the cytosine is sequenced as a 'T', and is thus unmethylated.

`nonconversion`:

  Object of class `"numeric"`. The (estimated) nonconversion rate (see Details) for each of the libraries.

### Details

The nonconversion slot is an estimate of the rate (for each library) at which an unmethylated cytosine has failed to be converted by sodium bisulphite treatment into thymine, and is thus recorded (incorrectly) as methylated. In some cases, this can be estimated from considering observed methylation rates on regions known to be unmethylated (e.g., chloroplasts) or by introducing unmethylated control sequences.

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 = "alignmentMeth")`: ...

dim

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

initialize

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

show

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

### Author(s)

Thomas J. Hardcastle

### See Also

`alignmentClass`, the class from which `'alignmentMeth'` inherits. `readMeths`, which will produce a `'alignmentMeth'` object from files generated by the YAMA aligner. `processAD`, which will convert an `'alignmentMeth'` object into a 'segData' object for segmentation.

[Package segmentSeq version 2.28.0 Index]