inheriting objects from free annotation files.track.table.GTF(file, name = NA, attr = "split", features = "exon", quiet = FALSE, ...)
track.exons.CCDS(file, name = "CCDS exons", ...)
track.CNV.DGV(file, name = "DGV CNV", ...)
track.genes.NCBI(file, name = "NCBI genes", selection, ...)
track.bands.UCSC(file, name = "UCSC bands", ...)
read.gtf
.
read.gtf
.
read.gtf
.
track.table
arguments. Consider notably .organism
and .assembly
for track annotation.
-inheriting object (of class
,
,
or
).track.table.GTF
imports a "Gene Feature Transfert" file, as proposed by the UCSC Table Browser at http://www.genome.ucsc.edu/cgi-bin/hgTables) for a large amount of species. See the read.gtf
manual for further details. track.exons.CCDS
contains various transcripts from the "Consensus Coding DNA Sequence" project, currently only available for mouse and human (see the NCBI data repository at http://ftp.ncbi.nlm.nih.gov/pub/CCDS/, and look for a file named "CCDS_current.txt"). track.CNV.DGV
parses constitutive copy number variations from the current version of the Database of Genomic Variants, downloadable from http://dgv.tcag.ca/dgv/app/downloads using "DGV Variants" links. The whole database is dedicated to the human specy only. track.genes.NCBI
parses the gene list from the MapView project of the NCBI, for one of many species available at http://ftp.ncbi.nih.gov/genomes/MapView/. Select your specy of interest, then browse "sequence", "current" and "initial_release" (if the directories are available, they are not for certain species). Download the file named "seq_gene.md.gz". As many assemblies are included in the file, a first call to the function without "selection" is required, to list the available values. A second call with the appropriate assembly name will produce the desired track file. track.bands.UCSC
produces a track of cytogenetic banding, as made available by the UCSC for many species at http://hgdownload.cse.ucsc.edu/downloads.html. Select the specy and assembly version that suits your needs, and look for a file named "cytoBand.txt.gz" in the "Annotation database" section.track.exons.CCDS
raw file (current human assembly) : http://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human/CCDS.current.txt Example of track.CNV.DGV
raw file (human assembly 'hg19') : http://dgv.tcag.ca/dgv/docs/GRCh37_hg19_variants_2013-05-31.txt Example of track.genes.NCBI
raw file (current human assembly) : http://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/sequence/current/initial_release/seq_gene.md.gz Example of track.bands.UCSC
raw file (human assembly 'hg19') : http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gztrack.fasta-constructors
, Annotation
track.table-class
, track.exons-class
, track.CNV-class
, track.genes-class
or track.bands-class
tk.browse
, browsePlot
# From the "How-to" vignette, section "Custom annotation tracks"
file <- system.file("extdata/Cosmic_ATM.gtf.gz", package="Rgb")
tt <- track.table.GTF(file)
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