getCytoband

Description

This function generates a data.frame with the respective cytoband names, chromosomes, Giemsa stain, and the start and end positions. These tables can then be used to plot chromosome idiograms. Currently, cytoband annotation for UCSC genome builds hg18 and hg19 are supported.

Usage

getCytoband(build)

Arguments

Value

data.frame

Author(s)

Michael Considine

See Also

plotIdiogram

Examples

cytoband <- getCytoband("hg19")
cytoband <- cytoband[cytoband$chr == "chr1", ]
plotIdiogram(1, "hg18", cytoband=cytoband, cex.axis=0.6)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(SNPchip)
Welcome to SNPchip version 2.18.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SNPchip/getCytoband.rd_%03d_medium.png", width=480, height=480)
> ### Name: getCytoband
> ### Title: getCytoband
> ### Aliases: getCytoband
> ### Keywords: misc
> 
> ### ** Examples
> 
> cytoband <- getCytoband("hg19")
> cytoband <- cytoband[cytoband$chr == "chr1", ]
> plotIdiogram(1, "hg18", cytoband=cytoband, cex.axis=0.6)
NULL
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>