CNVrd2-class {CNVrd2} | R Documentation

## Class `"CNVrd2"`

### Description

A class of reading BAM files into R and grouping read-count windows into similar segments.

### Objects from the Class

Objects can be created by calls of the form `new("CNVrd2", ...)`.

### Slots

`windows`:

  Object of class `"numeric"` indicating a window size.

`chr`:

  Object of class `"character"` indicating the chromosome of the region.

`st`:

  Object of class `"numeric"` indicating the starting coordinate of the region.

`en`:

  Object of class `"numeric"` indicating the ending coordinate of the region.

`dirBamFile`:

  Object of class `"character"` indicating a directory of BAM files.

`dirCoordinate`:

  Object of class `"character"` indicating a directory where all the positions of mapped reads will be written out to prepare for the segmentation process.

`genes`:

  Object of class `"numeric"` indicating gene coordinates.

`geneNames`:

  Object of class `"character"` indicating names of genes.

### Methods

countReadInWindow

  `signature(Object = "CNVrd2")`: Count reads in windows.

plotCNVrd2

  `signature(Object = "CNVrd2")`: Plot traces of samples.

segmentSamples

  `signature(Object = "CNVrd2")`: Cluster windows of read counts into regions having similar signal values.

### Author(s)

Hoang Tan Nguyen, Tony R Merriman and MA Black. hoangtannguyenvn@gmail.com

### Examples

    showClass("CNVrd2")

[Package CNVrd2 version 1.30.0 Index]