CNVrd2-class: Class '"CNVrd2"'

In CNVrd2: CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

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. [e-mail]

Examples

showClass("CNVrd2")

CNVrd2 documentation built on Nov. 8, 2020, 5:30 p.m.