BiomartGeneRegionTrack class and methods
Source:R/BiomartGeneRegionTrack-class.R
BiomartGeneRegionTrack-class.RdA class to hold gene model data for a genomic region fetched dynamically from EBI's Biomart Ensembl data source.
# S4 method for 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 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
Martobject 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
biomartargument 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, wherexmay 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
settingsand 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
getBMfor 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
Value
The return value of the constructor function is a new object of class
BiomartGeneRegionTrack.
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.
Functions
initialize(BiomartGeneRegionTrack): Initialize.BiomartGeneRegionTrack(): Constructor function forBiomartGeneRegionTrack-class.subset(BiomartGeneRegionTrack): subset aBiomartGeneRegionTrackby coordinates and sort if necessary.
Objects from the class
Objects can be created using the constructor function
BiomartGeneRegionTrack.
References
EBI Biomart webservice at http://www.biomart.org.
See also
Examples
# \dontshow{
## Load some sample data
data(bmTrack)
# }
## Construct the object
if (FALSE) {
bmTrack <- BiomartGeneRegionTrack(
start = 26682683, end = 26711643,
chromosome = 7, genome = "mm9"
)
}
# \dontshow{
## 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)
}
# }
## 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 name
#> <Rle> <IRanges> <Rle> | <character> <character>
#> [1] chr7 26682695-26711578 + | ENSMUST00000005477 Cyp2b10
#> [2] chr7 26682639-26711643 + | ENSMUST00000072438 Cyp2b10
#> [3] chr7 26701785-26702449 + | ENSMUST00000144140 Cyp2b10
#> itemRgb blockCount blockSizes blockStarts
#> <character> <numeric> <character> <character>
#> [1] gold4 10 180,163,150,161,177,.. 0,13562,13878,16189,..
#> [2] gold4 9 236,163,150,161,177,.. 0,13618,13934,16245,..
#> [3] gold4 2 356,143 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 ENSMUSE00000736922 ENSMUSE00000748299
#> "Cyp2b10" "Cyp2b10" "Cyp2b10"
#>
#> $rank
#> ENSMUSE00000742021 ENSMUSE00000449901 ENSMUSE00000199425
#> "1" "2" "3"
#> ENSMUSE00000511070 ENSMUSE00000514929 ENSMUSE00000199423
#> "4" "5" "6"
#> ENSMUSE00000535814 ENSMUSE00000507557 ENSMUSE00000498616
#> "7" "8" "9"
#> ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1
#> "1" "2" "3"
#> ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1
#> "4" "5" "6"
#> ENSMUSE00000535814.1 ENSMUSE00000507557.1 ENSMUSE00000496705
#> "7" "8" "9"
#> ENSMUSE00000750625 ENSMUSE00000736922 ENSMUSE00000748299
#> "10" "1" "2"
#>
#> $exonId
#> 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"
#>
#> $origExonId
#> 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"
#>
#> $col
#> ENSMUSE00000742021 ENSMUSE00000449901 ENSMUSE00000199425
#> "transparent" "transparent" "transparent"
#> ENSMUSE00000511070 ENSMUSE00000514929 ENSMUSE00000199423
#> "transparent" "transparent" "transparent"
#> ENSMUSE00000535814 ENSMUSE00000507557 ENSMUSE00000498616
#> "transparent" "transparent" "transparent"
#> ENSMUSE00000489385 ENSMUSE00000449901.1 ENSMUSE00000199425.1
#> "transparent" "transparent" "transparent"
#> ENSMUSE00000511070.1 ENSMUSE00000514929.1 ENSMUSE00000199423.1
#> "transparent" "transparent" "transparent"
#> ENSMUSE00000535814.1 ENSMUSE00000507557.1 ENSMUSE00000496705
#> "transparent" "transparent" "transparent"
#> ENSMUSE00000750625 ENSMUSE00000736922 ENSMUSE00000748299
#> "transparent" "transparent" "transparent"
#>
#> $title
#> [1] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
#> [8] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
#> [15] "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10" "Cyp2b10"
#>