genomemap: Create an interative genome map.

In D3GB: Interactive Genome Browser with R

Description

genomemap creates an interactive genome map.

Usage

genomemap(assembly, mapTrack = NA, dir = "GenomeMap")

Arguments

assembly	a genome assembly data frame. D3GB provides human assemblies (NCBI36, GRCh37, GRCh38), human assemblies with cytobands (GRCh37.bands or GRCh38.bands), or methods for creating your own assembly from a FASTA file getAssemblyFromFasta.
mapTrack	a data frame with values to represent on the genome map in BED format: chromosome, start, end, name, value.
dir	a "character" string representing the directory where the graph will be saved.

Value

The function creates a folder in your computer with an HTML document named index.html which contains the graph. This file can be directly opened with Firefox. If you want to open this file stored in your local machine with other Web browser, please visit the help section on the D3GB Web site (http://d3gb.usal.es).

Author(s)

David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/

See Also

The ‘D3GB’ Website: http://d3gb.usal.es

createAssembly, getAssemblyFromFasta, GRCh37.bands, GRCh38.bands.

Examples

genomemap(GRCh38.bands, dir="GRCh38_map")

D3GB documentation built on May 2, 2019, 9:42 a.m.