These functions constructs track.table
inheriting objects from free annotation files.
track.table.GTF(file, name = NA, attr = "split", features = "exon", quiet = FALSE,
.chromosomes, ...)
track.exons.CCDS(file, name = "CCDS exons", ...)
track.exons.GENCODE(file, name = "GENCODE exons",
extra = c("gene_id", "gene_name", "exon_id"), ...)
track.CNV.DGV(file, name = "DGV CNV", ...)
track.genes.NCBI(file, name = "NCBI genes", selection, ...)
track.bands.UCSC(file, name = "UCSC bands", ...)
Return a track.table
-inheriting object (of class track.exons
, track.CNV
, track.genes
or track.bands
).
Single character value, the path to the raw file to parse. See the 'Details' section below.
Single character value, the name
field for the track.table
object. For track.table.GTF
, use NA
to refer to the "source" column content (if it contains a unique value for all rows).
To be passed to read.gtf
.
To be passed to read.gtf
.
To be passed to read.gtf
.
To be passed to the track.table
constructor.
Further arguments are passed to the class constructor, as a result most of the handled arguments are track.table
arguments. Consider notably .organism
and .assembly
for track annotation.
Character vector, names of optional columns to keep from the GENCODE GTF file.
Character vector, filter to apply on the "group_label" column for NCBI genes. Raises an error with the possible values when missing.
Sylvain Mareschal
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 https://ftp.ncbi.nlm.nih.gov/pub/CCDS/, and look for a file named "CCDS_current.txt").
track.exons.GENCODE
contains various transcripts from the GENCODE project, currently only available for mouse and human (see the dedicated website at https://www.gencodegenes.org/). This function is intended to run on the GTF version of the data.
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 https://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.
Example of track.exons.CCDS
raw file (current human assembly) : https://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human/CCDS.current.txt
Example of track.exons.GENCODE
raw file (human assembly 'GRCh38') : ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz
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 (human assembly 'GRCh37') : https://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/sequence/BUILD.37.3/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.gz
track.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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