UcscTrack: Meta-constructor for Gviz tracks fetched directly from the...

In ivanek/Gviz: Plotting data and annotation information along genomic coordinates

Meta-constructor for Gviz tracks fetched directly from the various UCSC data sources.

Description

The UCSC data base provides a wealth of annotation information. This function can be used to access UCSC, to retrieve the data available there and to return it as an annotation track object amenable to plotting with plotTracks.

Usage

UcscTrack(
  track,
  table = NULL,
  trackType = c("AnnotationTrack", "GeneRegionTrack", "DataTrack", "GenomeAxisTrack"),
  genome,
  chromosome,
  name = NULL,
  from,
  to,
  ...
)

Arguments

track	Character, the name of the track to fetch from UCSC. To find out about available tracks please consult the online table browser at http://genome.ucsc.edu/cgi-bin/hgTables?command=start.
table	Character, the name of the table to fetch from UCSC, or NULL, in which case the default selection of tables is used. To find out about available tables for a given track please consult the online table browser at http://genome.ucsc.edu/cgi-bin/hgTables?command=start.
trackType	Character, one in c("AnnotationTrack", "GeneRegionTrack", "DataTrack", "GenomeAxisTrack"). The function will try to coerce the downloaded data in an object of this class. See below for details.
genome	Character, a valid USCS genome identifier for which to fetch the data.
chromosome	Character, a valid USCS character identifier for which to fetch the data.
name	Character, the name to use for the resulting track object.
from, to	A range of genomic locations for which to fetch data.
...	All additional named arguments are expected to be either display parameters for the resulting objects, or character scalars of column names in the downloaded UCSC data tables that are matched by name to available arguments in the respective constructor functions as defined by the trackType argument. See Details section for more information.

Details

clearSessionCache is can be called to remove all cached items from the session which are generated when connecting with the UCSC data base.

The data stored at the UCSC data bases can be of different formats: gene or transcript model data, simple annotation features like CpG Island locations or SNPs, or numeric data like conservation or mapability. This function presents a unified API to download all kinds of data and to map them back to one of the annotation track objects defined in this package. The type of object to hold the data has to be given in the trackType argument, and subsequently the function passes all data on to the respective object constructor. All additional named arguments are considered to be relevant for the constructor of choice, and single character scalars are replaced by the respective data columns in the downloaded UCSC tables if available. For instance, assuming the table for track 'foo' contains the columns 'id', 'type', 'fromLoc' and 'toLoc', giving the feature identifier, type, start end end location. In order to create an AnnotationTrack object from that data, we have to pass the additional named arguments id="id", feature="type", start="fromLoc" and codeend="toLoc" to the UcscTrack function. The complete function call could look like this:

UcscTrack(track="foo", genome="mm9", chromosome=3, from=1000, to=10000, trackType="AnnotationTrack", id="id", feature="type", start="from", end="to")

To reduce the bandwidth, some caching of the UCSC connection takes place. In order to remove these cached session items, call clearSessionCache.

The Gviz.ucscUrl option controls which URL is being used to connect to UCSC. For instance, one could switch to the European UCSC mirror by calling options(Gviz.ucscUrl="http://genome-euro.ucsc.edu/cgi-bin/".

Value

An annotation track object as determined by trackType.

Author(s)

Florian Hahne

See Also

AnnotationTrack

DataTrack

GeneRegionTrack

GenomeAxisTrack

plotTracks

Examples

## Not run: 

## Create UcscTrack for Known Genes from mm9 genome
from <- 65921878
to <- 65980988
knownGenes <- UcscTrack(
    genome = "mm9", chromosome = "chrX", track = "knownGene",
    from = from, to = to, trackType = "GeneRegionTrack",
    rstarts = "exonStarts", rends = "exonEnds", gene = "name",
    symbol = "name", transcript = "name", strand = "strand",
    fill = "#8282d2", name = "UCSC Genes"
)

## End(Not run)

## if the UCSC is not accessible load prepared object
data(ucscItems)

## knownGenes is essentially GeneRegionTrack
knownGenes

## plotting
plotTracks(knownGenes, chromosome = "chrX", from = 65920688, to = 65960068)

ivanek/Gviz documentation built on Nov. 20, 2023, 8:16 p.m.