getIdeoGR: Get ideogram information

In lawremi/biovizBase: Basic graphic utilities for visualization of genomic data.

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)

lawremi/biovizBase documentation built on Dec. 21, 2021, 9:42 a.m.