D3GB (version 1.1)

genome_addGFF: Add track in a gff file to

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.

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)
## ---------------------------------------------