Annotation: Annotation track constructors

In Rgb: The R Genome Browser

Annotation track constructors

Description

These functions constructs track.table inheriting objects from free annotation files.

Usage

  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", ...)

Arguments

file	Single character value, the path to the raw file to parse. See the 'Details' section below.
name	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).
attr	To be passed to read.gtf.
features	To be passed to read.gtf.
quiet	To be passed to read.gtf.
.chromosomes	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.
extra	Character vector, names of optional columns to keep from the GENCODE GTF file.
selection	Character vector, filter to apply on the "group_label" column for NCBI genes. Raises an error with the possible values when missing.

Details

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.

Value

Return a track.table-inheriting object (of class track.exons, track.CNV, track.genes or track.bands).

Author(s)

Sylvain Mareschal

References

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

See Also

track.fasta-constructors, Annotation

track.table-class, track.exons-class, track.CNV-class, track.genes-class or track.bands-class

tk.browse, browsePlot

Examples

  # From the "How-to" vignette, section "Custom annotation tracks"
  file <- system.file("extdata/Cosmic_ATM.gtf.gz", package="Rgb")
  tt <- track.table.GTF(file)

Rgb documentation built on Aug. 18, 2023, 5:05 p.m.