getIdeogram: Get ideogram.

Description Usage Arguments Details Value Author(s) Examples

View source: R/ideogram.R

Description

Get ideogram w/o cytoband for certain genome

Usage

1
getIdeogram(genome, subchr, cytobands=TRUE)

Arguments

genome

Single specie names, which must be one of the result from ucscGenomes()$db. If missing, will invoke a menu for users to choose from.

subchr

A character vector used to subset the result.

cytobands

If TRUE, return ideogram with gieStain and name column. If FALSE, simply return the genome information for each chromosome.

Details

This function require a network connection, it will parse the data on the fly, function is a wrapper of some functionality from rtracklayer package to get certain table like cytoBand, a full table schema could be found http://genome.ucsc.edu/cgi-bin/hgTables in UCSC genome browser.This is useful for visualization of the whole genome or single chromosome, you can see some examples in ggbio package.

Value

A GRanges object.

Author(s)

Tengfei Yin

Examples

1
## Not run: hg19IdeogramCyto <- getIdeogram("hg19", cytoband = TRUE)

Bioconductor-mirror/biovizBase documentation built on June 1, 2017, 5:21 a.m.