Annotation {Rgb} | R Documentation

## 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.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.
`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 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.

### 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) : 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 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)

[Package Rgb version 1.6.1 Index]