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Last data update: 2014.03.03

R: BiomartGeneRegionTrack class and methods

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


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

Arguments

`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.
`strand`	Character scalar, the strand for which to fetch gene information from Biomart. One in `+`, `-`, or `+-`.
`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.
`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.
`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.
`featureMap`	Named character vector to map between the fields in the Biomart data base and the features as they are used to construct the track.
`name`	Character scalar of the track's name used in the title panel when plotting.
`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.

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.

Objects from the class

Objects can be created using the constructor function BiomartGeneRegionTrack.

Slots

biomart:: Object of class "MartOrNULL", the connection to the Ensembl Biomart webservice.
filter:: Object of class "list", additional filters for the data base query.
start:: Object of class "numeric", inherited from class GeneRegionTrack. The start coordinates of the annotation range. The coorrdinates for the individual gene model items are stored in the range slot.
end:: Object of class "numeric", inherited from class GeneRegionTrack. The end coordinates of the annotation range. The corrdinates for the individual gene model items are stored in the range slot.
stacking:: Object of class "character", inherited from class StackedTrack
stacks:: Object of class "environment", inherited from class StackedTrack
range:: Object of class GRanges, inherited from class RangeTrack
chromosome:: Object of class "character", inherited from class RangeTrack
genome:: Object of class "character", inherited from class RangeTrack
dp:: Object of class DisplayPars, inherited from class GdObject
name:: Object of class "character", inherited from class GdObject
imageMap:: Object of class ImageMap, inherited from class GdObject

Extends

Class "GeneRegionTrack", directly.

Class "AnnotationTrack", by class "GeneRegionTrack", distance 2.

Class "StackedTrack", by class "GeneRegionTrack", distance 3.

Class "RangeTrack", by class "GeneRegionTrack", distance 4.

Class "GdObject", by class "GeneRegionTrack", distance 5.

Methods

In the following code chunks, obj is considered to be an object of class BiomartGeneRegionTrack.

Internal methods:

initialize: signature(.Object = "BiomartGeneRegionTrack"): initialize the object.

Inherited methods:

group

signature(gdObject="BiomartGeneRegionTrack"): extract the group membership for all track items.

Usage:

group(GdObject)

Examples:

: group(obj)

group<-

signature(gdObject="BiomartGeneRegionTrack", value="character"): replace the grouping information for track items. The replacement value must be a factor of appropriate length or another vector that can be coerced into such.

Usage:

group<-(GdObject, value)

Examples:

: group(obj) <- c("a", "a", "b", "c", "a")

identifier

signature(gdObject="BiomartGeneRegionTrack"): return track item identifiers. Depending on the setting of the optional argument lowest, these are either the group identifiers or the individual item identifiers.

Usage:

identifier(GdObject, lowest=FALSE)

Additional Arguments:

: lowest: return the lowest-level identifier, i.e., the item IDs, or the higher level group IDs which do not have to be unqiue.

Examples:

: identifier(obj, lowest=FALSE)

identifier<-

signature(gdObject="BiomartGeneRegionTrack", value="character"): Set the track item identifiers. The replacement value has to be a character vector of appropriate length. This always replaces the group-level identifiers, so essentially it is similar to groups<-.

Usage:

identifier<-(GdObject, value)

Examples:

: identifier(obj) <- c("foo", "bar")

exon

signature(GdObject="BiomartGeneRegionTrack"): Extract the exon identifiers for all exons in the gene models.

Usage:

exon(GdObject)

Examples:

: exon(obj)

exon<-

signature(GdObject="BiomartGeneRegionTrack", value="character"): replace the exon identifiers for all exons in the gene model. The replacement value must be a character of appropriate length or another vector that can be coerced into such.

Usage:

exon<-(GdObject, value)

Examples:

: exon(obj) <- paste("Exon", 1:5)

gene

signature(GdObject="BiomartGeneRegionTrack"): Extract the gene identifiers for all gene models.

Usage:

gene(GdObject)

Examples:

: gene(obj)

gene<-

signature(GdObject="BiomartGeneRegionTrack", value="character"): replace the gene identifiers for all gene models. The replacement value must be a character of appropriate length or another vector that can be coerced into such.

Usage:

gene<-(GdObject, value)

Examples:

: gene(obj) <- paste("Gene", LETTERS[1:5])

symbol

signature(GdObject="BiomartGeneRegionTrack"): Extract the human-readble gene symbol for all gene models.

Usage:

symbol(GdObject)

Examples:

: symbol(obj)

symbol<-

signature(GdObject="BiomartGeneRegionTrack", value="character"): replace the human-readable gene symbol for all gene models. The replacement value must be a character of appropriate length or another vector that can be coerced into such.

Usage:

gene<-(GdObject, value)

Examples:

: symbol(obj) <- letters[1:5]

transcript

signature(GdObject="BiomartGeneRegionTrack"): Extract the transcript identifiers for all transcripts in the gene models.

Usage:

transcript(GdObject)

Examples:

: transcript(obj)

transcript<-

signature(GdObject="BiomartGeneRegionTrack", value="character"): replace the transcript identifiers for all transcripts in the gene model. The replacement value must be a character of appropriate length or another vector that can be coerced into such.

Usage:

transcript<-(GdObject, value)

Examples:

: transcript(obj) <- paste("Exon", 1:5)

Internal methods:

coerce

signature(from="BiomartGeneRegionTrack", to="UCSCData"): coerce to a UCSCData object for export to the UCSC genome browser.

Examples:

: as(obj, "UCSCData")

collapseTrack

signature(GdObject="BiomartGeneRegionTrack"): preprocess the track before plotting. This will collapse overlapping track items based on the available resolution and increase the width and height of all track objects to a minimum value to avoid rendering issues. See collapsing for details.

Usage:

collapseTrack(GdObject, diff=.pxResolution(coord="x"))

Additional Arguments:

: diff: the minimum pixel width to display, everything below that will be inflated to a width of diff.

Examples:

: Gviz:::collapseTrack(obj)

show

signature(object="BiomartGeneRegionTrack"): show a human-readable summary of the object

drawGD

signature(GdObject="BiomartGeneRegionTrack"): plot the object to a graphics device. The return value of this method is the input object, potentially updated during the plotting operation. Internally, there are two modes in which the method can be called. Either in 'prepare' mode, in which case no plotting is done but the object is preprocessed based on the available space, or in 'plotting' mode, in which case the actual graphical output is created. Since subsetting of the object can be potentially costly, this can be switched off in case subsetting has already been performed before or is not necessary.

Usage:

drawGD(GdObject, minBase, maxBase, prepare=FALSE, subset=TRUE, ...)

Additional Arguments:

: minBase, maxBase: the coordinate range to plot.
: prepare: run method in preparation or in production mode.
: subset: subset the object to the visible region or skip the potentially expensive subsetting operation.
: ...: all further arguments are ignored.

Examples:

: Gviz:::drawGD(obj)
: Gviz:::drawGD(obj, minBase=1, maxBase=100)
: Gviz:::drawGD(obj, prepare=TRUE, subset=FALSE)

drawGrid

signature(GdObject="BiomartGeneRegionTrack"): superpose a grid on top of a track.

Usage:

drawGrid(GdObject, from, to)

Additional Arguments:

: from, to: integer scalars, draw grid within a certain coordinates range. This needs to be supplied for the plotting function to know the current genomic coordinates.

Examples:

: Gviz:::drawGrid(obj, from=10, to=100)

setStacks

signature(GdObject="BiomartGeneRegionTrack"): recompute the stacks based on the available space and on the object's track items and stacking settings.

Usage:

setStacks(GdObject, from, to)

Additional Arguments:

: from, to: integer scalars, compute stacking within a certain coordinates range. This needs to be supplied for the plotting function to know the current genomic coordinates.

Examples:

: Gviz:::setStacks(obj, from=1, to=100)

stacking

signature(GdObject="BiomartGeneRegionTrack"): return the current stacking type.

Usage:

stacking(GdObject)

Examples:

: stacking(obj)

stacking<-

signature(GdObject="BiomartGeneRegionTrack", value="character"): set the object's stacking type to one in c(hide, dense, squish, pack,full).

Usage:

stacking<-(GdObject, value)

Additional Arguments:

: value: replacement value.

Examples:

: stacking(obj) <- "squish"

stacks

signature(GdObject="BiomartGeneRegionTrack"): return the stack indices for each track item.

Usage:

stacks(GdObject)

Examples:

: Gviz:::stacks(obj)

[

signature(x="BiomartGeneRegionTrack", i="ANY", j="ANY", drop="ANY"): subset the items in the BiomartGeneRegionTrack object. This is essentially similar to subsetting of the GRanges object in the range slot. For most applications, the subset method may be more appropriate.

Additional Arguments:

: i, j: subsetting indices, j is ignored.
: drop: argument is ignored.

Examples:

: obj[1:5]

chromosome

signature(GdObject="BiomartGeneRegionTrack"): return the chromosome for which the track is defined.

Usage:

chromosome(GdObject)

Examples:

: chromosome(obj)

chromosome<-

signature(GdObject="BiomartGeneRegionTrack"): replace the value of the track's chromosome. This has to be a valid UCSC chromosome identifier or an integer or character scalar that can be reasonably coerced into one.

Usage:

chromosome<-(GdObject, value)

Additional Arguments:

: value: replacement value.

Examples:

: chromosome(obj) <- "chr12"

start, end, width

signature(x="BiomartGeneRegionTrack"): the start or end coordinates of the track items, or their width in genomic coordinates.

Usage:

start(x)

end(x)

width(x)

Examples:

: start(obj)
: end(obj)
: width(obj)

start<-, end<-, width<-

signature(x="BiomartGeneRegionTrack"): replace the start or end coordinates of the track items, or their width.

Usage:

start<-(x, value)

end<-(x, value)

width<-(x, value)

Additional Arguments:

: value: replacement value.

Examples:

: start(obj) <- 1:10
: end(obj) <- 20:30
: width(obj) <- 1

position

signature(GdObject="BiomartGeneRegionTrack"): the arithmetic mean of the track item's coordionates, i.e., (end(obj)-start(obj))/2.

Usage:

position(GdObject)

Examples:

: position(obj)

feature

signature(GdObject="BiomartGeneRegionTrack"): return the grouping information for track items. For certain sub-classes, groups may be indicated by different color schemes when plotting. See grouping for details.

Usage:

feature(GdObject)

Examples:

: feature(obj)

feature<-

signature(gdObject="BiomartGeneRegionTrack", value="character"): set the grouping information for track items. This has to be a factor vector (or another type of vector that can be coerced into one) of the same length as the number of items in the BiomartGeneRegionTrack. See grouping for details.

Usage:

feature<-(GdObject, value)

Additional Arguments:

: value: replacement value.

Examples:

: feature(obj) <- c("a", "a", "b", "c", "a")

genome

signature(x="BiomartGeneRegionTrack"): return the track's genome.

Usage:

genome(x)

Examples:

: genome(obj)

genome<-

signature(x="BiomartGeneRegionTrack"): set the track's genome. Usually this has to be a valid UCSC identifier, however this is not formally enforced here.

Usage:

genome<-(x, value)

Additional Arguments:

: value: replacement value.

Examples:

: genome(obj) <- "mm9"

length

signature(x="BiomartGeneRegionTrack"): return the number of items in the track.

Usage:

length(x)

Examples:

: length(obj)

range

signature(x="BiomartGeneRegionTrack"): return the genomic coordinates for the track as an object of class IRanges.

Usage:

range(x)

Examples:

: range(obj)

ranges

signature(x="BiomartGeneRegionTrack"): return the genomic coordinates for the track along with all additional annotation information as an object of class GRanges.

Usage:

ranges(x)

Examples:

: ranges(obj)

split

signature(x="BiomartGeneRegionTrack"): split a BiomartGeneRegionTrack object by an appropriate factor vector (or another vector that can be coerced into one). The output of this operation is a list of objects of the same class as the input object, all inheriting from class BiomartGeneRegionTrack.

Usage:

split(x, f, ...)

Additional Arguments:

: f: the splitting factor.
: ...: all further arguments are ignored.

Examples:

: split(obj, c("a", "a", "b", "c", "a"))

strand

signature(x="BiomartGeneRegionTrack"): return a vector of strand specifiers for all track items, in the form '+' for the Watson strand, '-' for the Crick strand or '*' for either of the two.

Usage:

strand(x)

Examples:

: strand(obj)

strand<-

signature(x="BiomartGeneRegionTrack"): replace the strand information for the track items. The replacement value needs to be an appropriate scalar or vector of strand values.

Usage:

strand<-(x, value)

Additional Arguments:

: value: replacement value.

Examples:

: strand(obj) <- "+"

values

signature(x="BiomartGeneRegionTrack"): return all additional annotation information except for the genomic coordinates for the track items as a data.frame.

Usage:

values(x)

Examples:

: values(obj)

coerce

signature(from="BiomartGeneRegionTrack", to="data.frame"): coerce the GRanges object in the range slot into a regular data.frame.

Examples:

: as(obj, "data.frame")

subset

signature(x="BiomartGeneRegionTrack"): subset a BiomartGeneRegionTrack by coordinates and sort if necessary.

Usage:

subset(x, from, to, sort=FALSE, ...)

Additional Arguments:

: from, to: the coordinates range to subset to.
: sort: sort the object after subsetting. Usually not necessary.
: ...: additional arguments are ignored.

Examples:

: subset(obj, from=10, to=20, sort=TRUE)

displayPars

signature(x="BiomartGeneRegionTrack", name="character"): list the value of the display parameter name. See settings for details on display parameters and customization.

Usage:

displayPars(x, name)

Examples:

: displayPars(obj, "col")

displayPars

signature(x="BiomartGeneRegionTrack", name="missing"): list the value of all available display parameters. See settings for details on display parameters and customization.

Examples:

: displayPars(obj)

getPar

signature(x="BiomartGeneRegionTrack", name="character"): alias for the displayPars method. See settings for details on display parameters and customization.

Usage:

getPar(x, name)

Examples:

: getPar(obj, "col")

getPar

signature(x="BiomartGeneRegionTrack", name="missing"): alias for the displayPars method. See settings for details on display parameters and customization.

Examples:

: getPar(obj)

displayPars<-

signature(x="BiomartGeneRegionTrack", value="list"): set display parameters using the values of the named list in value. See settings for details on display parameters and customization.

Usage:

displayPars<-(x, value)

Examples:

: displayPars(obj) <- list(col="red", lwd=2)

setPar

signature(x="BiomartGeneRegionTrack", value="character"): set the single display parameter name to value. Note that display parameters in the BiomartGeneRegionTrack class are pass-by-reference, so no re-assignmnet to the symbol obj is necessary. See settings for details on display parameters and customization.

Usage:

setPar(x, name, value)

Additional Arguments:

: name: the name of the display parameter to set.

Examples:

: setPar(obj, "col", "red")

setPar

signature(x="BiomartGeneRegionTrack", value="list"): set display parameters by the values of the named list in value. Note that display parameters in the BiomartGeneRegionTrack class are pass-by-reference, so no re-assignmnet to the symbol obj is necessary. See settings for details on display parameters and customization.

Examples:

: setPar(obj, list(col="red", lwd=2))

names

signature(x="BiomartGeneRegionTrack"): return the value of the name slot.

Usage:

names(x)

Examples:

: names(obj)

names<-

signature(x="BiomartGeneRegionTrack", value="character"): set the value of the name slot.

Usage:

names<-(x, value)

Examples:

: names(obj) <- "foo"

coords

signature(ImageMap="BiomartGeneRegionTrack"): return the coordinates from the internal image map.

Usage:

coords(ImageMap)

Examples:

: coords(obj)

tags

signature(x="BiomartGeneRegionTrack"): return the tags from the internal image map.

Usage:

tags(x)

Examples:

: tags(obj)

Display Parameters

The following display parameters are set for objects of class BiomartGeneRegionTrack upon instantiation, unless one or more of them have already been set by one of the optional sub-class initializers, which always get precedence over these global defaults. See settings for details on setting graphical parameters for tracks.

: C_segment="burlywood4": Character or integer scalar. Fill color for annotation objects of type 'C_segment'.
: D_segment="lightblue": Character or integer scalar. Fill color for annotation objects of type 'C_segment'.
: J_segment="dodgerblue2": Character or integer scalar. Fill color for annotation objects of type 'C_segment'.
: miRNA="cornflowerblue": Character or integer scalar. Fill color for annotation objects of type 'L_segment'.
: miRNA_pseudogene="cornsilk": Character or integer scalar. Fill color for annotation objects of type 'miRNA_pseudogene'.
: misc_RNA="cornsilk3": Character or integer scalar. Fill color for annotation objects of type 'misc_RNA'.
: misc_RNA_pseudogene="cornsilk4": Character or integer scalar. Fill color for annotation objects of type 'misc_RNA_pseudogene'.
: Mt_rRNA="yellow": Character or integer scalar. Fill color for annotation objects of type 'Mt_rRNA'.
: Mt_tRNA="darkgoldenrod": Character or integer scalar. Fill color for annotation objects of type 'Mt_tRNA'.
: Mt_tRNA_pseudogene="darkgoldenrod1": Character or integer scalar. Fill color for annotation objects of type 'Mt_tRNA_pseudogene'.
: protein_coding="gold4": Character or integer scalar. Fill color for annotation objects of type 'protein_coding'.
: pseudogene="brown1": Character or integer scalar. Fill color for annotation objects of type 'pseudogene'.
: retrotransposed="blueviolet": Character or integer scalar. Fill color for annotation objects of type 'retrotransposed'.
: rRNA="darkolivegreen1": Character or integer scalar. Fill color for annotation objects of type 'rRNA'.
: rRNA_pseudogene="darkolivegreen": Character or integer scalar. Fill color for annotation objects of type 'rRNA_pseudogene'.
: scRNA="darkorange": Character or integer scalar. Fill color for annotation objects of type 'scRNA'.
: scRNA_pseudogene="darkorange2": Character or integer scalar. Fill color for annotation objects of type 'scRNA_pseudogene'.
: snoRNA="cyan": Character or integer scalar. Fill color for annotation objects of type 'snoRNA'.
: snoRNA_pseudogene="cyan2": Character or integer scalar. Fill color for annotation objects of type 'snoRNA_pseudogene'.
: snRNA="coral": Character or integer scalar. Fill color for annotation objects of type 'snRNA'.
: snRNA_pseudogene="coral3": Character or integer scalar. Fill color for annotation objects of type 'snRNA_pseudogene'.
: tRNA_pseudogene="antiquewhite3": Character or integer scalar. Fill color for annotation objects of type 'tRNA_pseudogene'.
: V_segment="aquamarine": Character or integer scalar. Fill color for annotation objects of type 'V_segment'.

Additional display parameters are being inherited from the respective parent classes. Note that not all of them may have an effect on the plotting of BiomartGeneRegionTrack objects.

GeneRegionTrack:

: fill="orange": Character or integer scalar. The fill color for untyped items. This is also used to connect grouped items. See grouping for details.
: geneSymbols=TRUE: Logical scalar. Use human-readable gene symbols or gene IDs for the transcript annotation.
: shape=c("smallArrow", "box"): Character scalar. The shape in which to display the track items. Currently only box, arrow, ellipse, and smallArrow are implemented.
: showExonId=FALSE: Logical scalar. Control whether to plot the individual exon identifiers.
: collapseTranscripts=FALSE: Logical or character scalar. Can be one in gene, longest, shortest or meta. Merge all transcripts of the same gene into one single gene model. In the case of gene (or TRUE), this will only keep the start location of the first exon and the end location of the last exon from all transcripts of the gene. For shortest and longest, only the longest or shortest transcript model is retained. For meta, a meta-transcript containing the union of all exons is formed (essentially identical to the operation reduce(geneModel)).
: thinBoxFeature=c("utr", "ncRNA", "utr3", "utr5", "miRNA", "lincRNA"): Character vector. A listing of feature types that should be drawn with thin boxes. Typically those are non-coding elements.

AnnotationTrack:

: cex=1: Numeric scalar. The font expansion factor for item identifiers.
: cex.group=0.6: Numeric scalar. The font expansion factor for the group-level annotation.
: col="transparent": Character or integer scalar. The border color for all track items.
: fontcolor="white": Character or integer scalar. The font color for item identifiers.
: fontcolor.group="#808080": Character or integer scalar. The font color for the group-level annotation.
: fontface=1: Integer scalar. The font face for item identifiers.
: fontface.group=2: Numeric scalar. The font face for the group-level annotation.
: fontfamily="sans": Character scalar. The font family for item identifiers.
: fontsize=12: Numeric scalar. The font size for item identifiers.
: lex=1: Numeric scalar. The line expansion factor for all track items. This is also used to connect grouped items. See grouping for details.
: lineheight=1: Numeric scalar. The font line height for item identifiers.
: lty="solid": Character or integer scalar. The line type for all track items. This is also used to connect grouped items. See grouping for details.
: lwd=1: Integer scalar. The line width for all track items. This is also used to connect grouped items. See grouping for details.
: rotation=0: Numeric scalar. The degree of text rotation for item identifiers.
: showFeatureId=FALSE: Logical scalar. Control whether to plot the individual track item identifiers.
: showId=FALSE: Logical scalar. Control whether to annotate individual groups.
: showOverplotting=FALSE: Logical scalar. Use a color gradient to show the amount of overplotting for collapsed items. This implies that collapse==TRUE
: size=1: Numeric scalar. The relative size of the track. Can be overridden in the plotTracks function.
: mergeGroups=FALSE: Logical scalar. Merge fully overlapping groups if collapse==TRUE.

StackedTrack:

: reverseStacking=FALSE: Logical flag. Reverse the y-ordering of stacked items. I.e., features that are plotted on the bottom-most stacks will be moved to the top-most stack and vice versa.
: stackHeight=0.75: Numeric between 0 and 1. Controls the vertical size and spacing between stacked elements. The number defines the proportion of the total available space for the stack that is used to draw the glyphs. E.g., a value of 0.5 means that half of the available vertical drawing space (for each stacking line) is used for the glyphs, and thus one quarter of the available space each is used for spacing above and below the glyph. Defaults to 0.75.

GdObject:

: alpha=1: Numeric scalar. The transparency for all track items.
: background.panel="transparent": Integer or character scalar. The background color of the content panel.
: background.title="lightgray": Integer or character scalar. The background color for the title panels.
: col.border.title="transparent": Integer or character scalar. The border color for the title panels.
: lwd.border.title=1: Integer scalar. The border width for the title panels.
: cex.axis=NULL: Numeric scalar. The expansion factor for the axis annotation. Defaults to NULL, in which case it is computed based on the available space.
: cex.title=NULL: Numeric scalar. The expansion factor for the title panel. This effects the fontsize of both the title and the axis, if any. Defaults to NULL, which means that the text size is automatically adjusted to the available space.
: col.axis="white": Integer or character scalar. The font and line color for the y axis, if any.
: col.frame="lightgray": Integer or character scalar. The line color used for the panel frame, if frame==TRUE
: col.grid="#808080": Integer or character scalar. Default line color for grid lines, both when type=="g" in DataTracks and when display parameter grid==TRUE.
: col.line=NULL: Integer or character scalar. Default colors for plot lines. Usually the same as the global col parameter.
: col.symbol=NULL: Integer or character scalar. Default colors for plot symbols. Usually the same as the global col parameter.
: col.title="white": Integer or character scalar. The font color for the title panels.
: collapse=TRUE: Boolean controlling wether to collapse the content of the track to accomodate the minimum current device resolution. See collapsing for details.
: fontface.title=2: Integer or character scalar. The font face for the title panels.
: fontfamily.title="sans": Integer or character scalar. The font family for the title panels.
: frame=FALSE: Boolean. Draw a frame around the track when plotting.
: grid=FALSE: Boolean, switching on/off the plotting of a grid.
: h=-1: Integer scalar. Parameter controlling the number of horizontal grid lines, see panel.grid for details.
: lty.grid="solid": Integer or character scalar. Default line type for grid lines, both when type=="g" in DataTracks and when display parameter grid==TRUE.
: lwd.grid=1: Numeric scalar. Default line width for grid lines, both when type=="g" in DataTracks and when display parameter grid==TRUE.
: min.distance=1: Numeric scalar. The minimum pixel distance before collapsing range items, only if collapse==TRUE. See collapsing for details.
: min.height=3: Numeric scalar. The minimum range height in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See collapsing for details.
: min.width=1: Numeric scalar. The minimum range width in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See collapsing for details.
: showAxis=TRUE: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).
: showTitle=TRUE: Boolean controlling whether to plot a title panel. Although this can be set individually for each track, in multi-track plots as created by plotTracks there will still be an empty placeholder in case any of the other tracks include a title. The same holds true for axes. Note that the the title panel background color could be set to transparent in order to completely hide it.
: v=-1: Integer scalar. Parameter controlling the number of vertical grid lines, see panel.grid for details.

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Gviz)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Gviz/BiomartGeneRegionTrack-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BiomartGeneRegionTrack-class
> ### Title: BiomartGeneRegionTrack class and methods
> ### Aliases: BiomartGeneRegionTrack-class BiomartGeneRegionTrack
> ###   initialize,BiomartGeneRegionTrack-method
> ###   subset,BiomartGeneRegionTrack-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> 
> ## Don't show: 
> ## Load some sample data
> data(bmTrack)
> ## End(Don't show)
> 
> ## Construct the object
> ## Not run: 
> ##D bmTrack <- BiomartGeneRegionTrack(start=26682683, end=26711643,
> ##D chromosome=7, genome="mm9")
> ## End(Not run)
> 
> ## Don't show: 
> ## For some annoying reason the postscript device does not know about
> ## the sans font
> #if(!interactive())
> #{
> font <- ps.options()$family
> displayPars(bmTrack) <- list(fontfamily=font, fontfamily.title=font)
> #}
> ## End(Don't show)
> 
> ## Plotting
> plotTracks(bmTrack)
> 
> ## Track names
> names(bmTrack)
[1] "BiomartGeneRegionTrack"
> names(bmTrack) <- "foo"
> plotTracks(bmTrack)
> 
> ## Subsetting and splitting
> subTrack <- subset(bmTrack, from=26700000, to=26705000)
> length(subTrack)
[1] 21
> subTrack <- bmTrack[transcript(bmTrack)=="ENSMUST00000144140"]
> split(bmTrack, transcript(bmTrack))
$ENSMUST00000005477
GeneRegionTrack 'foo'
| genome: mm9
| active chromosome: chr7
| annotation features: 10

$ENSMUST00000072438
GeneRegionTrack 'foo'
| genome: mm9
| active chromosome: chr7
| annotation features: 9

$ENSMUST00000144140
GeneRegionTrack 'foo'
| genome: mm9
| active chromosome: chr7
| annotation features: 2

> 
> ## Accessors
> start(bmTrack)
 [1] 26682639 26696257 26696573 26698884 26699767 26700411 26701953 26702307
 [9] 26711087 26682695 26696257 26696573 26698884 26699767 26700411 26701953
[17] 26702307 26710392 26711087 26701785 26702307
> end(bmTrack)
 [1] 26682874 26696419 26696722 26699044 26699943 26700552 26702140 26702448
 [9] 26711643 26682874 26696419 26696722 26699044 26699943 26700552 26702140
[17] 26702448 26710418 26711578 26702140 26702449
> width(bmTrack)
 [1] 236 163 150 161 177 142 188 142 557 180 163 150 161 177 142 188 142  27 492
[20] 356 143
> position(bmTrack)
 [1] 26682756 26696338 26696648 26698964 26699855 26700482 26702046 26702378
 [9] 26711365 26682784 26696338 26696648 26698964 26699855 26700482 26702046
[17] 26702378 26710405 26711332 26701962 26702378
> width(subTrack) <- width(subTrack)+100
> 
> strand(bmTrack)
 [1] "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+" "+"
[20] "+" "+"
> strand(subTrack) <- "-"
> 
> chromosome(bmTrack)
  chr7 
"chr7" 
> chromosome(subTrack) <- "chrX"
> 
> genome(bmTrack)
[1] "mm9"
> genome(subTrack) <- "hg19"
> 
> range(bmTrack)
IRanges object with 21 ranges and 0 metadata columns:
           start       end     width
       <integer> <integer> <integer>
   [1]  26682639  26682874       236
   [2]  26696257  26696419       163
   [3]  26696573  26696722       150
   [4]  26698884  26699044       161
   [5]  26699767  26699943       177
   ...       ...       ...       ...
  [17]  26702307  26702448       142
  [18]  26710392  26710418        27
  [19]  26711087  26711578       492
  [20]  26701785  26702140       356
  [21]  26702307  26702449       143
> ranges(bmTrack)
GRanges object with 21 ranges and 6 metadata columns:
       seqnames               ranges strand |        feature               gene
          <Rle>            <IRanges>  <Rle> |    <character>        <character>
   [1]     chr7 [26682639, 26682874]      + | protein_coding ENSMUSG00000030483
   [2]     chr7 [26696257, 26696419]      + | protein_coding ENSMUSG00000030483
   [3]     chr7 [26696573, 26696722]      + | protein_coding ENSMUSG00000030483
   [4]     chr7 [26698884, 26699044]      + | protein_coding ENSMUSG00000030483
   [5]     chr7 [26699767, 26699943]      + | protein_coding ENSMUSG00000030483
   ...      ...                  ...    ... .            ...                ...
  [17]     chr7 [26702307, 26702448]      + | protein_coding ENSMUSG00000030483
  [18]     chr7 [26710392, 26710418]      + | protein_coding ENSMUSG00000030483
  [19]     chr7 [26711087, 26711578]      + | protein_coding ENSMUSG00000030483
  [20]     chr7 [26701785, 26702140]      + | protein_coding ENSMUSG00000030483
  [21]     chr7 [26702307, 26702449]      + | protein_coding ENSMUSG00000030483
                     exon         transcript      symbol      rank
              <character>        <character> <character> <numeric>
   [1] ENSMUSE00000742021 ENSMUST00000072438     Cyp2b10         1
   [2] ENSMUSE00000449901 ENSMUST00000072438     Cyp2b10         2
   [3] ENSMUSE00000199425 ENSMUST00000072438     Cyp2b10         3
   [4] ENSMUSE00000511070 ENSMUST00000072438     Cyp2b10         4
   [5] ENSMUSE00000514929 ENSMUST00000072438     Cyp2b10         5
   ...                ...                ...         ...       ...
  [17] ENSMUSE00000507557 ENSMUST00000005477     Cyp2b10         8
  [18] ENSMUSE00000496705 ENSMUST00000005477     Cyp2b10         9
  [19] ENSMUSE00000750625 ENSMUST00000005477     Cyp2b10        10
  [20] ENSMUSE00000736922 ENSMUST00000144140     Cyp2b10         1
  [21] ENSMUSE00000748299 ENSMUST00000144140     Cyp2b10         2
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> ## Annotation
> identifier(bmTrack)
 [1] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
 [8] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
[15] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
> identifier(bmTrack, "lowest")
 [1] "ENSMUSE00000742021" "ENSMUSE00000449901" "ENSMUSE00000199425"
 [4] "ENSMUSE00000511070" "ENSMUSE00000514929" "ENSMUSE00000199423"
 [7] "ENSMUSE00000535814" "ENSMUSE00000507557" "ENSMUSE00000498616"
[10] "ENSMUSE00000489385" "ENSMUSE00000449901" "ENSMUSE00000199425"
[13] "ENSMUSE00000511070" "ENSMUSE00000514929" "ENSMUSE00000199423"
[16] "ENSMUSE00000535814" "ENSMUSE00000507557" "ENSMUSE00000496705"
[19] "ENSMUSE00000750625" "ENSMUSE00000736922" "ENSMUSE00000748299"
> identifier(subTrack) <- "bar"
> 
> feature(bmTrack)
 [1] "protein_coding" "protein_coding" "protein_coding" "protein_coding"
 [5] "protein_coding" "protein_coding" "protein_coding" "protein_coding"
 [9] "protein_coding" "protein_coding" "protein_coding" "protein_coding"
[13] "protein_coding" "protein_coding" "protein_coding" "protein_coding"
[17] "protein_coding" "protein_coding" "protein_coding" "protein_coding"
[21] "protein_coding"
> feature(subTrack) <- "foo"
> 
> exon(bmTrack)
 [1] "ENSMUSE00000742021" "ENSMUSE00000449901" "ENSMUSE00000199425"
 [4] "ENSMUSE00000511070" "ENSMUSE00000514929" "ENSMUSE00000199423"
 [7] "ENSMUSE00000535814" "ENSMUSE00000507557" "ENSMUSE00000498616"
[10] "ENSMUSE00000489385" "ENSMUSE00000449901" "ENSMUSE00000199425"
[13] "ENSMUSE00000511070" "ENSMUSE00000514929" "ENSMUSE00000199423"
[16] "ENSMUSE00000535814" "ENSMUSE00000507557" "ENSMUSE00000496705"
[19] "ENSMUSE00000750625" "ENSMUSE00000736922" "ENSMUSE00000748299"
> exon(subTrack) <- letters[1:2]
> 
> gene(bmTrack)
 [1] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
 [4] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
 [7] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
[10] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
[13] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
[16] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
[19] "ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483"
> gene(subTrack) <- "bar"
> 
> symbol(bmTrack)
 [1] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
 [8] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
[15] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
> symbol(subTrack) <- "foo"
> 
> transcript(bmTrack)
 [1] "ENSMUST00000072438" "ENSMUST00000072438" "ENSMUST00000072438"
 [4] "ENSMUST00000072438" "ENSMUST00000072438" "ENSMUST00000072438"
 [7] "ENSMUST00000072438" "ENSMUST00000072438" "ENSMUST00000072438"
[10] "ENSMUST00000005477" "ENSMUST00000005477" "ENSMUST00000005477"
[13] "ENSMUST00000005477" "ENSMUST00000005477" "ENSMUST00000005477"
[16] "ENSMUST00000005477" "ENSMUST00000005477" "ENSMUST00000005477"
[19] "ENSMUST00000005477" "ENSMUST00000144140" "ENSMUST00000144140"
> transcript(subTrack) <- c("foo", "bar")
> chromosome(subTrack) <- "chr7"
> plotTracks(subTrack)
> 
> values(bmTrack)
          feature               gene               exon         transcript
1  protein_coding ENSMUSG00000030483 ENSMUSE00000742021 ENSMUST00000072438
2  protein_coding ENSMUSG00000030483 ENSMUSE00000449901 ENSMUST00000072438
3  protein_coding ENSMUSG00000030483 ENSMUSE00000199425 ENSMUST00000072438
4  protein_coding ENSMUSG00000030483 ENSMUSE00000511070 ENSMUST00000072438
5  protein_coding ENSMUSG00000030483 ENSMUSE00000514929 ENSMUST00000072438
6  protein_coding ENSMUSG00000030483 ENSMUSE00000199423 ENSMUST00000072438
7  protein_coding ENSMUSG00000030483 ENSMUSE00000535814 ENSMUST00000072438
8  protein_coding ENSMUSG00000030483 ENSMUSE00000507557 ENSMUST00000072438
9  protein_coding ENSMUSG00000030483 ENSMUSE00000498616 ENSMUST00000072438
10 protein_coding ENSMUSG00000030483 ENSMUSE00000489385 ENSMUST00000005477
11 protein_coding ENSMUSG00000030483 ENSMUSE00000449901 ENSMUST00000005477
12 protein_coding ENSMUSG00000030483 ENSMUSE00000199425 ENSMUST00000005477
13 protein_coding ENSMUSG00000030483 ENSMUSE00000511070 ENSMUST00000005477
14 protein_coding ENSMUSG00000030483 ENSMUSE00000514929 ENSMUST00000005477
15 protein_coding ENSMUSG00000030483 ENSMUSE00000199423 ENSMUST00000005477
16 protein_coding ENSMUSG00000030483 ENSMUSE00000535814 ENSMUST00000005477
17 protein_coding ENSMUSG00000030483 ENSMUSE00000507557 ENSMUST00000005477
18 protein_coding ENSMUSG00000030483 ENSMUSE00000496705 ENSMUST00000005477
19 protein_coding ENSMUSG00000030483 ENSMUSE00000750625 ENSMUST00000005477
20 protein_coding ENSMUSG00000030483 ENSMUSE00000736922 ENSMUST00000144140
21 protein_coding ENSMUSG00000030483 ENSMUSE00000748299 ENSMUST00000144140
    symbol rank
1  Cyp2b10    1
2  Cyp2b10    2
3  Cyp2b10    3
4  Cyp2b10    4
5  Cyp2b10    5
6  Cyp2b10    6
7  Cyp2b10    7
8  Cyp2b10    8
9  Cyp2b10    9
10 Cyp2b10    1
11 Cyp2b10    2
12 Cyp2b10    3
13 Cyp2b10    4
14 Cyp2b10    5
15 Cyp2b10    6
16 Cyp2b10    7
17 Cyp2b10    8
18 Cyp2b10    9
19 Cyp2b10   10
20 Cyp2b10    1
21 Cyp2b10    2
> 
> ## Grouping
> group(bmTrack)
 [1] "ENSMUST00000072438" "ENSMUST00000072438" "ENSMUST00000072438"
 [4] "ENSMUST00000072438" "ENSMUST00000072438" "ENSMUST00000072438"
 [7] "ENSMUST00000072438" "ENSMUST00000072438" "ENSMUST00000072438"
[10] "ENSMUST00000005477" "ENSMUST00000005477" "ENSMUST00000005477"
[13] "ENSMUST00000005477" "ENSMUST00000005477" "ENSMUST00000005477"
[16] "ENSMUST00000005477" "ENSMUST00000005477" "ENSMUST00000005477"
[19] "ENSMUST00000005477" "ENSMUST00000144140" "ENSMUST00000144140"
> group(subTrack) <- "Group 1"
> transcript(subTrack)
[1] "Group 1" "Group 1"
> plotTracks(subTrack)
> 
> ## Stacking
> stacking(bmTrack)
[1] "squish"
> stacking(bmTrack) <- "dense"
> plotTracks(bmTrack)
> 
> ## coercion
> as(bmTrack, "data.frame")
   X.seqnames  X.start    X.end X.width X.strand      X.feature
1        chr7 26682639 26682874     236        + protein_coding
2        chr7 26696257 26696419     163        + protein_coding
3        chr7 26696573 26696722     150        + protein_coding
4        chr7 26698884 26699044     161        + protein_coding
5        chr7 26699767 26699943     177        + protein_coding
6        chr7 26700411 26700552     142        + protein_coding
7        chr7 26701953 26702140     188        + protein_coding
8        chr7 26702307 26702448     142        + protein_coding
9        chr7 26711087 26711643     557        + protein_coding
10       chr7 26682695 26682874     180        + protein_coding
11       chr7 26696257 26696419     163        + protein_coding
12       chr7 26696573 26696722     150        + protein_coding
13       chr7 26698884 26699044     161        + protein_coding
14       chr7 26699767 26699943     177        + protein_coding
15       chr7 26700411 26700552     142        + protein_coding
16       chr7 26701953 26702140     188        + protein_coding
17       chr7 26702307 26702448     142        + protein_coding
18       chr7 26710392 26710418      27        + protein_coding
19       chr7 26711087 26711578     492        + protein_coding
20       chr7 26701785 26702140     356        + protein_coding
21       chr7 26702307 26702449     143        + protein_coding
               X.gene             X.exon       X.transcript X.symbol X.rank
1  ENSMUSG00000030483 ENSMUSE00000742021 ENSMUST00000072438  Cyp2b10      1
2  ENSMUSG00000030483 ENSMUSE00000449901 ENSMUST00000072438  Cyp2b10      2
3  ENSMUSG00000030483 ENSMUSE00000199425 ENSMUST00000072438  Cyp2b10      3
4  ENSMUSG00000030483 ENSMUSE00000511070 ENSMUST00000072438  Cyp2b10      4
5  ENSMUSG00000030483 ENSMUSE00000514929 ENSMUST00000072438  Cyp2b10      5
6  ENSMUSG00000030483 ENSMUSE00000199423 ENSMUST00000072438  Cyp2b10      6
7  ENSMUSG00000030483 ENSMUSE00000535814 ENSMUST00000072438  Cyp2b10      7
8  ENSMUSG00000030483 ENSMUSE00000507557 ENSMUST00000072438  Cyp2b10      8
9  ENSMUSG00000030483 ENSMUSE00000498616 ENSMUST00000072438  Cyp2b10      9
10 ENSMUSG00000030483 ENSMUSE00000489385 ENSMUST00000005477  Cyp2b10      1
11 ENSMUSG00000030483 ENSMUSE00000449901 ENSMUST00000005477  Cyp2b10      2
12 ENSMUSG00000030483 ENSMUSE00000199425 ENSMUST00000005477  Cyp2b10      3
13 ENSMUSG00000030483 ENSMUSE00000511070 ENSMUST00000005477  Cyp2b10      4
14 ENSMUSG00000030483 ENSMUSE00000514929 ENSMUST00000005477  Cyp2b10      5
15 ENSMUSG00000030483 ENSMUSE00000199423 ENSMUST00000005477  Cyp2b10      6
16 ENSMUSG00000030483 ENSMUSE00000535814 ENSMUST00000005477  Cyp2b10      7
17 ENSMUSG00000030483 ENSMUSE00000507557 ENSMUST00000005477  Cyp2b10      8
18 ENSMUSG00000030483 ENSMUSE00000496705 ENSMUST00000005477  Cyp2b10      9
19 ENSMUSG00000030483 ENSMUSE00000750625 ENSMUST00000005477  Cyp2b10     10
20 ENSMUSG00000030483 ENSMUSE00000736922 ENSMUST00000144140  Cyp2b10      1
21 ENSMUSG00000030483 ENSMUSE00000748299 ENSMUST00000144140  Cyp2b10      2
          feature               gene               exon         transcript
1  protein_coding ENSMUSG00000030483 ENSMUSE00000742021 ENSMUST00000072438
2  protein_coding ENSMUSG00000030483 ENSMUSE00000449901 ENSMUST00000072438
3  protein_coding ENSMUSG00000030483 ENSMUSE00000199425 ENSMUST00000072438
4  protein_coding ENSMUSG00000030483 ENSMUSE00000511070 ENSMUST00000072438
5  protein_coding ENSMUSG00000030483 ENSMUSE00000514929 ENSMUST00000072438
6  protein_coding ENSMUSG00000030483 ENSMUSE00000199423 ENSMUST00000072438
7  protein_coding ENSMUSG00000030483 ENSMUSE00000535814 ENSMUST00000072438
8  protein_coding ENSMUSG00000030483 ENSMUSE00000507557 ENSMUST00000072438
9  protein_coding ENSMUSG00000030483 ENSMUSE00000498616 ENSMUST00000072438
10 protein_coding ENSMUSG00000030483 ENSMUSE00000489385 ENSMUST00000005477
11 protein_coding ENSMUSG00000030483 ENSMUSE00000449901 ENSMUST00000005477
12 protein_coding ENSMUSG00000030483 ENSMUSE00000199425 ENSMUST00000005477
13 protein_coding ENSMUSG00000030483 ENSMUSE00000511070 ENSMUST00000005477
14 protein_coding ENSMUSG00000030483 ENSMUSE00000514929 ENSMUST00000005477
15 protein_coding ENSMUSG00000030483 ENSMUSE00000199423 ENSMUST00000005477
16 protein_coding ENSMUSG00000030483 ENSMUSE00000535814 ENSMUST00000005477
17 protein_coding ENSMUSG00000030483 ENSMUSE00000507557 ENSMUST00000005477
18 protein_coding ENSMUSG00000030483 ENSMUSE00000496705 ENSMUST00000005477
19 protein_coding ENSMUSG00000030483 ENSMUSE00000750625 ENSMUST00000005477
20 protein_coding ENSMUSG00000030483 ENSMUSE00000736922 ENSMUST00000144140
21 protein_coding ENSMUSG00000030483 ENSMUSE00000748299 ENSMUST00000144140
    symbol rank
1  Cyp2b10    1
2  Cyp2b10    2
3  Cyp2b10    3
4  Cyp2b10    4
5  Cyp2b10    5
6  Cyp2b10    6
7  Cyp2b10    7
8  Cyp2b10    8
9  Cyp2b10    9
10 Cyp2b10    1
11 Cyp2b10    2
12 Cyp2b10    3
13 Cyp2b10    4
14 Cyp2b10    5
15 Cyp2b10    6
16 Cyp2b10    7
17 Cyp2b10    8
18 Cyp2b10    9
19 Cyp2b10   10
20 Cyp2b10    1
21 Cyp2b10    2
> as(bmTrack, "UCSCData")
UCSC track 'foo'
UCSCData object with 3 ranges and 6 metadata columns:
                     seqnames               ranges strand |                 id
                        <Rle>            <IRanges>  <Rle> |        <character>
  ENSMUST00000005477     chr7 [26682695, 26711578]      + | ENSMUST00000005477
  ENSMUST00000072438     chr7 [26682639, 26711643]      + | ENSMUST00000072438
  ENSMUST00000144140     chr7 [26701785, 26702449]      + | ENSMUST00000144140
                            name     itemRgb blockCount
                     <character> <character>  <integer>
  ENSMUST00000005477     Cyp2b10       gold4         10
  ENSMUST00000072438     Cyp2b10       gold4          9
  ENSMUST00000144140     Cyp2b10       gold4          2
                                                 blockSizes
                                                <character>
  ENSMUST00000005477 180,163,150,161,177,142,188,142,27,492
  ENSMUST00000072438    236,163,150,161,177,142,188,142,557
  ENSMUST00000144140                                356,143
                                                                 blockStarts
                                                                 <character>
  ENSMUST00000005477 0,13562,13878,16189,17072,17716,19258,19612,27697,28392
  ENSMUST00000072438       0,13618,13934,16245,17128,17772,19314,19668,28448
  ENSMUST00000144140                                                   0,522
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> 
> ## HTML image map
> coords(bmTrack)
NULL
> tags(bmTrack)
NULL
> bmTrack <- plotTracks(bmTrack)$foo
> coords(bmTrack)
                            x1   y1        x2    y2
ENSMUSE00000742021    38.32764 64.5  41.79997 415.5
ENSMUSE00000449901   239.54551 64.5 241.93921 415.5
ENSMUSE00000199425   244.21469 64.5 246.41630 415.5
ENSMUSE00000511070   278.36174 64.5 280.72588 415.5
ENSMUSE00000514929   291.40884 64.5 294.00939 415.5
ENSMUSE00000199423   300.92450 64.5 303.00790 415.5
ENSMUSE00000535814   323.70890 64.5 326.47199 415.5
ENSMUSE00000507557   328.93956 64.5 331.02296 415.5
ENSMUSE00000498616   458.67175 64.5 466.88714 415.5
ENSMUSE00000489385    39.15509 64.5  41.79997 415.5
ENSMUSE00000449901.1 239.54551 64.5 241.93921 415.5
ENSMUSE00000199425.1 244.21469 64.5 246.41630 415.5
ENSMUSE00000511070.1 278.36174 64.5 280.72588 415.5
ENSMUSE00000514929.1 291.40884 64.5 294.00939 415.5
ENSMUSE00000199423.1 300.92450 64.5 303.00790 415.5
ENSMUSE00000535814.1 323.70890 64.5 326.47199 415.5
ENSMUSE00000507557.1 328.93956 64.5 331.02296 415.5
ENSMUSE00000496705   448.09222 64.5 449.08221 415.5
ENSMUSE00000750625   458.67175 64.5 465.92671 415.5
ENSMUSE00000736922   321.22656 64.5 326.47199 415.5
ENSMUSE00000748299   328.93956 64.5 331.03774 415.5
> tags(bmTrack)
$fill
  ENSMUSE00000742021   ENSMUSE00000449901   ENSMUSE00000199425 
             "gold4"              "gold4"              "gold4" 
  ENSMUSE00000511070   ENSMUSE00000514929   ENSMUSE00000199423 
             "gold4"              "gold4"              "gold4" 
  ENSMUSE00000535814   ENSMUSE00000507557   ENSMUSE00000498616 
             "gold4"              "gold4"              "gold4" 
  ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1 
             "gold4"              "gold4"              "gold4" 
ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1 
             "gold4"              "gold4"              "gold4" 
ENSMUSE00000535814.1 ENSMUSE00000507557.1   ENSMUSE00000496705 
             "gold4"              "gold4"              "gold4" 
  ENSMUSE00000750625   ENSMUSE00000736922   ENSMUSE00000748299 
             "gold4"              "gold4"              "gold4" 

$strand
  ENSMUSE00000742021   ENSMUSE00000449901   ENSMUSE00000199425 
                 "+"                  "+"                  "+" 
  ENSMUSE00000511070   ENSMUSE00000514929   ENSMUSE00000199423 
                 "+"                  "+"                  "+" 
  ENSMUSE00000535814   ENSMUSE00000507557   ENSMUSE00000498616 
                 "+"                  "+"                  "+" 
  ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1 
                 "+"                  "+"                  "+" 
ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1 
                 "+"                  "+"                  "+" 
ENSMUSE00000535814.1 ENSMUSE00000507557.1   ENSMUSE00000496705 
                 "+"                  "+"                  "+" 
  ENSMUSE00000750625   ENSMUSE00000736922   ENSMUSE00000748299 
                 "+"                  "+"                  "+" 

$text
  ENSMUSE00000742021   ENSMUSE00000449901   ENSMUSE00000199425 
"ENSMUSE00000742021" "ENSMUSE00000449901" "ENSMUSE00000199425" 
  ENSMUSE00000511070   ENSMUSE00000514929   ENSMUSE00000199423 
"ENSMUSE00000511070" "ENSMUSE00000514929" "ENSMUSE00000199423" 
  ENSMUSE00000535814   ENSMUSE00000507557   ENSMUSE00000498616 
"ENSMUSE00000535814" "ENSMUSE00000507557" "ENSMUSE00000498616" 
  ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1 
"ENSMUSE00000489385" "ENSMUSE00000449901" "ENSMUSE00000199425" 
ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1 
"ENSMUSE00000511070" "ENSMUSE00000514929" "ENSMUSE00000199423" 
ENSMUSE00000535814.1 ENSMUSE00000507557.1   ENSMUSE00000496705 
"ENSMUSE00000535814" "ENSMUSE00000507557" "ENSMUSE00000496705" 
  ENSMUSE00000750625   ENSMUSE00000736922   ENSMUSE00000748299 
"ENSMUSE00000750625" "ENSMUSE00000736922" "ENSMUSE00000748299" 

$start
  ENSMUSE00000742021   ENSMUSE00000449901   ENSMUSE00000199425 
          "26682639"           "26696257"           "26696573" 
  ENSMUSE00000511070   ENSMUSE00000514929   ENSMUSE00000199423 
          "26698884"           "26699767"           "26700411" 
  ENSMUSE00000535814   ENSMUSE00000507557   ENSMUSE00000498616 
          "26701953"           "26702307"           "26711087" 
  ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1 
          "26682695"           "26696257"           "26696573" 
ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1 
          "26698884"           "26699767"           "26700411" 
ENSMUSE00000535814.1 ENSMUSE00000507557.1   ENSMUSE00000496705 
          "26701953"           "26702307"           "26710371" 
  ENSMUSE00000750625   ENSMUSE00000736922   ENSMUSE00000748299 
          "26711087"           "26701785"           "26702307" 

$end
  ENSMUSE00000742021   ENSMUSE00000449901   ENSMUSE00000199425 
          "26682874"           "26696419"           "26696722" 
  ENSMUSE00000511070   ENSMUSE00000514929   ENSMUSE00000199423 
          "26699044"           "26699943"           "26700552" 
  ENSMUSE00000535814   ENSMUSE00000507557   ENSMUSE00000498616 
          "26702140"           "26702448"           "26711643" 
  ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1 
          "26682874"           "26696419"           "26696722" 
ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1 
          "26699044"           "26699943"           "26700552" 
ENSMUSE00000535814.1 ENSMUSE00000507557.1   ENSMUSE00000496705 
          "26702140"           "26702448"           "26710438" 
  ENSMUSE00000750625   ENSMUSE00000736922   ENSMUSE00000748299 
          "26711578"           "26702140"           "26702449" 

$feature
  ENSMUSE00000742021   ENSMUSE00000449901   ENSMUSE00000199425 
    "protein_coding"     "protein_coding"     "protein_coding" 
  ENSMUSE00000511070   ENSMUSE00000514929   ENSMUSE00000199423 
    "protein_coding"     "protein_coding"     "protein_coding" 
  ENSMUSE00000535814   ENSMUSE00000507557   ENSMUSE00000498616 
    "protein_coding"     "protein_coding"     "protein_coding" 
  ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1 
    "protein_coding"     "protein_coding"     "protein_coding" 
ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1 
    "protein_coding"     "protein_coding"     "protein_coding" 
ENSMUSE00000535814.1 ENSMUSE00000507557.1   ENSMUSE00000496705 
    "protein_coding"     "protein_coding"     "protein_coding" 
  ENSMUSE00000750625   ENSMUSE00000736922   ENSMUSE00000748299 
    "protein_coding"     "protein_coding"     "protein_coding" 

$gene
  ENSMUSE00000742021   ENSMUSE00000449901   ENSMUSE00000199425 
"ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483" 
  ENSMUSE00000511070   ENSMUSE00000514929   ENSMUSE00000199423 
"ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483" 
  ENSMUSE00000535814   ENSMUSE00000507557   ENSMUSE00000498616 
"ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483" 
  ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1 
"ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483" 
ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1 
"ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483" 
ENSMUSE00000535814.1 ENSMUSE00000507557.1   ENSMUSE00000496705 
"ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483" 
  ENSMUSE00000750625   ENSMUSE00000736922   ENSMUSE00000748299 
"ENSMUSG00000030483" "ENSMUSG00000030483" "ENSMUSG00000030483" 

$exon
  ENSMUSE00000742021   ENSMUSE00000449901   ENSMUSE00000199425 
"ENSMUSE00000742021" "ENSMUSE00000449901" "ENSMUSE00000199425" 
  ENSMUSE00000511070   ENSMUSE00000514929   ENSMUSE00000199423 
"ENSMUSE00000511070" "ENSMUSE00000514929" "ENSMUSE00000199423" 
  ENSMUSE00000535814   ENSMUSE00000507557   ENSMUSE00000498616 
"ENSMUSE00000535814" "ENSMUSE00000507557" "ENSMUSE00000498616" 
  ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1 
"ENSMUSE00000489385" "ENSMUSE00000449901" "ENSMUSE00000199425" 
ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1 
"ENSMUSE00000511070" "ENSMUSE00000514929" "ENSMUSE00000199423" 
ENSMUSE00000535814.1 ENSMUSE00000507557.1   ENSMUSE00000496705 
"ENSMUSE00000535814" "ENSMUSE00000507557" "ENSMUSE00000496705" 
  ENSMUSE00000750625   ENSMUSE00000736922   ENSMUSE00000748299 
"ENSMUSE00000750625" "ENSMUSE00000736922" "ENSMUSE00000748299" 

$transcript
  ENSMUSE00000742021   ENSMUSE00000449901   ENSMUSE00000199425 
"ENSMUST00000072438" "ENSMUST00000072438" "ENSMUST00000072438" 
  ENSMUSE00000511070   ENSMUSE00000514929   ENSMUSE00000199423 
"ENSMUST00000072438" "ENSMUST00000072438" "ENSMUST00000072438" 
  ENSMUSE00000535814   ENSMUSE00000507557   ENSMUSE00000498616 
"ENSMUST00000072438" "ENSMUST00000072438" "ENSMUST00000072438" 
  ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1 
"ENSMUST00000005477" "ENSMUST00000005477" "ENSMUST00000005477" 
ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1 
"ENSMUST00000005477" "ENSMUST00000005477" "ENSMUST00000005477" 
ENSMUSE00000535814.1 ENSMUSE00000507557.1   ENSMUSE00000496705 
"ENSMUST00000005477" "ENSMUST00000005477" "ENSMUST00000005477" 
  ENSMUSE00000750625   ENSMUSE00000736922   ENSMUSE00000748299 
"ENSMUST00000005477" "ENSMUST00000144140" "ENSMUST00000144140" 

$symbol
  ENSMUSE00000742021   ENSMUSE00000449901   ENSMUSE00000199425 
           "Cyp2b10"            "Cyp2b10"            "Cyp2b10" 
  ENSMUSE00000511070   ENSMUSE00000514929   ENSMUSE00000199423 
           "Cyp2b10"            "Cyp2b10"            "Cyp2b10" 
  ENSMUSE00000535814   ENSMUSE00000507557   ENSMUSE00000498616 
           "Cyp2b10"            "Cyp2b10"            "Cyp2b10" 
  ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1 
           "Cyp2b10"            "Cyp2b10"            "Cyp2b10" 
ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1 
           "Cyp2b10"            "Cyp2b10"            "Cyp2b10" 
ENSMUSE00000535814.1 ENSMUSE00000507557.1   ENSMUSE00000496705 
           "Cyp2b10"            "Cyp2b10"            "Cyp2b10" 
  ENSMUSE00000750625   ENSMUSE0

BiomartGeneRegionTrack class and methods

Description

Usage

Arguments

Details

Value

Objects from the class

Slots

Extends

Methods

Display Parameters

Author(s)

References

See Also

Examples

Results