genome_addGFF: Add track in a gff file to 'genomebrowser'.

In D3GB: Interactive Genome Browser

Add track in a gff file to genomebrowser.

Description

genome_addGFF add track in a gff file to genomebrowser.

Usage

genome_addGFF(gb, gfffile)

Arguments

gb	a genome browser object produced by the function genomebrowser.
gfffile	a "character" string representing the input gff file to be represented in the genome browser.

Value

No return value, called for side effects

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

genomebrowser, genome_addSequence, genome_addTrack, genome_addVCF.

Examples

# Download fasta file
fasta <- tempfile()
download.file(paste0("https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/297/395/",
"GCF_000297395.2_ASM29739v2/GCF_000297395.2_ASM29739v2_genomic.fna.gz"),fasta)

# Genome browser generation.
gb <- genomebrowser(getAssemblyFromFasta(fasta))

genome_addSequence(gb,fasta)

# Download gff file and add to the genome browser
gff <- tempfile()
download.file(paste0("https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/297/395/",
"GCF_000297395.2_ASM29739v2/GCF_000297395.2_ASM29739v2_genomic.gff.gz"),gff)

genome_addGFF(gb,gff)

plot(gb)

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