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

In D3GB: Interactive Genome Browser with R

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

The function add track in a gff file to 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

genomebrowser, genome_addSequence, genome_addTrack, genome_addVCF.

Examples

## Not run: 
# Download fasta file
fasta <- tempfile()
download.file(paste0("ftp://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.
# It creates a genome browser ready to be viewed in Firefox.
# For a server version, ready to be shared with Apache as a Website, set the parameter server=True
gb <- genomebrowser(getAssemblyFromFasta(fasta), dir = "Micromonospora_gff")

genome_addSequence(gb,fasta)

# Download gff file and add to the genome browser
gff <- tempfile()
download.file(paste0("ftp://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)

## End(Not run)

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