Chromosome-class | R Documentation |
Chromosome
ClassA class to represent a single chromsome in order to plot an image of the Giemsa-stained cytobands.
Chromosome(I, res = 2500, maxbase = 250000000)
## S4 method for signature 'Chromosome'
image(x, horiz = FALSE, mai = NULL, showBandNames = FALSE, ...)
I |
A human chromosome identifier; one of the values in |
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 |
horiz |
A logical value: should the image of the chromsome be oriented horizontally. |
mai |
margin inches, as in the usual graphical argument to |
showBandNames |
logical; shold the names of the bands be written on the plot? |
... |
Additional arguments to the image method; ignored. |
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..
The Chromosome
constructor returns an object of the
Chromosome
class. The image
method invisibly returns its
first argument.
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.
signature(object = "RCytoGPS")
Creates an image of the chromosme, with bands colored according
to Giemsa staining.
Kevin R. Coombes krc@silicovore.com, Dwayne G. Tally dtally110@hotmail.com
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.
x <- Chromosome(6)
image(x)
image(x, showBandNames = TRUE)
image(x, horiz = TRUE)
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