BiomartGeneRegionTrack-class: BiomartGeneRegionTrack class and methods
In ivanek/Gviz: Plotting data and annotation information along genomic coordinates

BiomartGeneRegionTrack-class

R Documentation

BiomartGeneRegionTrack class and methods

Description

A class to hold gene model data for a genomic region fetched dynamically from EBI's Biomart Ensembl data source.

Usage

## S4 method for signature 'BiomartGeneRegionTrack'
initialize(
  .Object,
  start = NULL,
  end = NULL,
  biomart,
  filter = list(),
  range,
  genome = NULL,
  chromosome = NULL,
  strand = NULL,
  featureMap = NULL,
  symbol = NULL,
  gene = NULL,
  transcript = NULL,
  entrez = NULL,
  ...
)

BiomartGeneRegionTrack(
  start = NULL,
  end = NULL,
  biomart,
  chromosome = NULL,
  strand,
  genome = NULL,
  stacking = "squish",
  filters = list(),
  featureMap = NULL,
  name = "BiomartGeneRegionTrack",
  symbol = NULL,
  gene = NULL,
  entrez = NULL,
  transcript = NULL,
  ...
)

## S4 method for signature 'BiomartGeneRegionTrack'
subset(x, from, to, chromosome, use.defaults = TRUE, ...)

Arguments

`.Object`	.Object
`start`	An integer scalar with the genomic start coordinates for the gene model range.
`end`	An integer scalar with the genomic end coordinates for the gene model range.
`biomart`	An optional `Mart` object providing access to the EBI Biomart webservice. As default the appropriate Ensembl data source is selected based on the provided genome and chromosome.
`filter`	filter
`range`	range
`genome`	The genome on which the track's ranges are defined. Usually this is a valid UCSC genome identifier, however this is not being formally checked at this point. If no mapping from genome to Biomart Ensembl data source is possible, the `biomart` argument needs to be provided by the user.
`chromosome`	The chromosome on which the track's genomic ranges are defined. A valid UCSC chromosome identifier. Please note that at this stage only syntactic checking takes place, i.e., the argument value needs to be a single integer, numeric character or a character of the form `chrx`, where `x` may be any possible string. The user has to make sure that the respective chromosome is indeed defined for the the track's genome.
`strand`	Character scalar, the strand for which to fetch gene information from Biomart. One in `+`, `-`, or `+-`.
`featureMap`	Named character vector or list to map between the fields in the Biomart data base and the features as they are used to construct the track. If multiple values are provided in a single list item, the package will use the first one that is defined in the selected Biomart.
`symbol, transcript, gene, entrez`	Character vector giving one or several gene symbols, Ensembl transcript identifiers, Ensembl gene identifiers, or ENTREZ gene identifiers, respectively. The genomic locus of their gene model will be fetch from Biomart instead of providing explicit start and end coordinates.
`...`	Additional items which will all be interpreted as further display parameters. See `settings` and the "Display Parameters" section below for details.
`stacking`	The stacking type for overlapping items of the track. One in `c(hide, dense, squish, pack,full)`. Currently, only hide (don't show the track items, squish (make best use of the available space) and dense (no stacking at all) are implemented.
`filters`	A list of additional filters to be applied in the Biomart query. See `getBM` for details.
`name`	Character scalar of the track's name used in the title panel when plotting.
`x`	A valid track object class name, or the object itself, in which case the class is derived directly from it.
`from, to`	from, to
`use.defaults`	`logical`

Details

A track containing all gene models in a particular region as fetched from EBI's Biomart service. Usually the user does not have to take care of the Biomart connection, which will be established automatically based on the provided genome and chromosome information. However, for full flexibility a valid Mart object may be passed on to the constructor. Please note that this assumes a connection to one of the Ensembl gene data sources, mapping the available query data back to the internal object slots.

Value

The return value of the constructor function is a new object of class BiomartGeneRegionTrack.

Functions

initialize(BiomartGeneRegionTrack): Initialize.
BiomartGeneRegionTrack(): Constructor function for BiomartGeneRegionTrack-class.
subset(BiomartGeneRegionTrack): subset a BiomartGeneRegionTrack by coordinates and sort if necessary.

Objects from the class

Objects can be created using the constructor function BiomartGeneRegionTrack.

Author(s)

Florian Hahne

References

EBI Biomart webservice at http://www.biomart.org.

Examples



## Construct the object
## Not run: 
bmTrack <- BiomartGeneRegionTrack(
    start = 26682683, end = 26711643,
    chromosome = 7, genome = "mm9"
)

## End(Not run)



## Plotting
plotTracks(bmTrack)

## Track names
names(bmTrack)
names(bmTrack) <- "foo"
plotTracks(bmTrack)

## Subsetting and splitting
subTrack <- subset(bmTrack, from = 26700000, to = 26705000)
length(subTrack)
subTrack <- bmTrack[transcript(bmTrack) == "ENSMUST00000144140"]
split(bmTrack, transcript(bmTrack))

## Accessors
start(bmTrack)
end(bmTrack)
width(bmTrack)
position(bmTrack)
width(subTrack) <- width(subTrack) + 100

strand(bmTrack)
strand(subTrack) <- "-"

chromosome(bmTrack)
chromosome(subTrack) <- "chrX"

genome(bmTrack)
genome(subTrack) <- "hg19"

range(bmTrack)
ranges(bmTrack)

## Annotation
identifier(bmTrack)
identifier(bmTrack, "lowest")
identifier(subTrack) <- "bar"

feature(bmTrack)
feature(subTrack) <- "foo"

exon(bmTrack)
exon(subTrack) <- letters[1:2]

gene(bmTrack)
gene(subTrack) <- "bar"

symbol(bmTrack)
symbol(subTrack) <- "foo"

transcript(bmTrack)
transcript(subTrack) <- c("foo", "bar")
chromosome(subTrack) <- "chr7"
plotTracks(subTrack)

values(bmTrack)

## Grouping
group(bmTrack)
group(subTrack) <- "Group 1"
transcript(subTrack)
plotTracks(subTrack)

## Stacking
stacking(bmTrack)
stacking(bmTrack) <- "dense"
plotTracks(bmTrack)

## coercion
as(bmTrack, "data.frame")
as(bmTrack, "UCSCData")

## HTML image map
coords(bmTrack)
tags(bmTrack)
bmTrack <- plotTracks(bmTrack)$foo
coords(bmTrack)
tags(bmTrack)

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