getIdeoGR {biovizBase} | R Documentation

## Get ideogram information

### Description

This function tries to parse ideogram information from `seqlengths` of a `GRanges` object. This information is usually used to plot chromosome background for kaytogram or esitmate proper lengths of chromosomes from data space for showing overview.

### Usage

       getIdeoGR(gr)

### Arguments

`gr` | A `GRanges` object with or without lengths information.

### Value

A ideogram `GRanges` object, each row indicate one single chromosome, and start with 1 and end with real chromosome length or estimated lengths.

### Author(s)

Tengfei Yin

### Examples

       library(GenomicRanges)
       data("hg19IdeogramCyto", package = "biovizBase")
       hg19IdeogramCyto
       ## without seqlengths, simply reduce
       getIdeoGR(hg19IdeogramCyto)
       ## with seqlengths
       gr <- GRanges("chr1",  IRanges(1,3))
       seqlevels(gr) <- c("chr1", "chr2", "chr3")
       nms <- c(100, 200, 300)
       names(nms) <- c("chr1", "chr2", "chr3")
       seqlengths(gr) <- nms
       gr
       getIdeoGR(gr)

[Package biovizBase version 1.34.1 Index]