Chromosome-class {RCytoGPS}

The Chromosome Class

Description

A class to represent a single chromsome in order to plot an image of the Giemsa-stained cytobands.

Usage

Chromosome(I, res = 2500, maxbase = 250000000)
## S4 method for signature 'Chromosome'
image(x, horiz = FALSE, mai = NULL, showBandNames = FALSE, ...)

Arguments

I

A human chromosome identifier; one of the values in c(1:22,"X", "Y").

res

An integer resolution; the number of pixels used to represent an entire chromosome.

maxbase

An integer representing an upper bound on the length of the longest chromosome, mneasured in base-pairs.

x

An object of the Chromosome class.

horiz

A logical value: should the image of the chromsome be oriented horizontally.

mai

margin inches, as in the usual graphical argument to par.

showBandNames

logical; shold the names of the bands be written on the plot?

...

Additional arguments to the image method; ignored.

Details

Conventional karyotyping describes chromosomal abnormalities (in a standardized text-based nomenclature) that are visible through a microsope. Karyotyping relies on a technique known as Giemsa staining, which creates a banding pattern along the chromosome of different shades of gray. This class is used to plot images of individual chromosomes, corectly reflecting the size and color of the bands..

Value

The Chromosome constructor returns an object of the Chromosome class. The image method invisibly returns its first argument.

Slots

name:

A character value, typically of the form "chr1".

label:

A chartacter value, typiclly of the form "Chr 1".

grid:

An integer vector (of length res) repesenting the base position along the chromosome.

range:

An integer vector of length 2 marking teh starting and ending position of the banded part of the chromosome, in bases.

stain:

An integer vector (of length res), where the values indicate the color of the Giemsa stain for that part of the chromosome.

Methods

image:

signature(object = "RCytoGPS") Creates an image of the chromosme, with bands colored according to Giemsa staining.

Author(s)

Kevin R. Coombes [e-mail], Dwayne G. Tally [e-mail]

References

Abrams ZB, Tally DG, Coombes KR. RCytoGPS: An R Package for Analyzing and Visualizing Cytogenetic Data. In preparation.

Abrams ZB, Tally DG, Zhang L, Coombes CE, Payne PRO, Abruzzo LV, Coombes KR. Pattern recognition in lymphoid malignancies using CytoGPS and Mercator. Under review.

Examples

x <- Chromosome(6)
image(x)
image(x, showBandNames = TRUE)
image(x, horiz = TRUE)