genomebrowser: Generates an interactive genome browser.

In D3GB: Interactive Genome Browser

Generates an interactive genome browser.

Description

genomebrowser creates an interactive genome browser.

Usage

genomebrowser(assembly, tracks = NULL, types = NA, colors = NA, mapTrack = NULL)

Arguments

tracks	a list of data frames with track information that will be viewed in the genome browser. These data frames should have a BED format with the following columns: chromosome/scaffold, start, end, name, score, strand.
types	a "character" vector with type of tracks that will be represented. It should be one of: "gene", "exons", "domain", "value" or "score".
colors	a "character" vector with color used for the track representation.
mapTrack	a data frame with values to represent on the genome map in BED format: chromosome, start, end, name, value.
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.

Value

Object of class genomebrowser.

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, genome_addGFF, genome_addSequence, genome_addTrack, genome_addVCF.

Examples

# Genome browser generation.
gb <- genomebrowser(GRCh38.bands)
# Now you can add sequences, tracks, gff or vcf

D3GB documentation built on June 22, 2024, 9:35 a.m.