Rgb (version 1.5.1)

Annotation:

Description

These functions constructs inheriting objects from free annotation files.

Usage

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", ...)

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 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.
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.
selection
Character vector, filter to apply on the "group_label" column for NCBI genes. Raises an error with the possible values when missing.

Value

Return a -inheriting object (of class , , or ).

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 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.

References

Example of 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.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

Run this code
  # 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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