Description Constructor Accessor Methods Data Access Author(s) Examples
The TrackHub
class represents a TrackHub data source,
essentially directory layout separating tracks and sequences by
genome, along with a few metadata files. This interface abstracts
those details and provides access to a TrackHub at any URL supported
by R (HTTP, FTP, and local files). This is an easy way to make data
accessible to the UCSC Genome Browser.
TrackHub(uri, create = FALSE)
: Constructs a
new TrackHub
object, representing a repository at
uri
. If create
is TRUE
, and uri
is
writeable (i.e., local), the repository is created if it does not
already exist. If it does exist, then a message is emitted to
indicate that the repository was not recreated.
In the code snippets below, x
represents a TrackHub
object.
x$genome
, x[["genome"]]
: Get
the TrackHubGenome
object for the genome named
genome
.
length(x)
: number of genomes in the repository.
uri(x)
:
Get the URI pointing to the TrackHub repository.
genome(x)
:
Get the identifiers of the genomes present in the repository.
writeTrackHub(x)
:
Write hub content and genomes from memory representation to the hub file and genomes file.
It also create resources if they are missing like genomes file and genome directory for
newly add genome.
Note that all storing methods(like hub()<-
) are only supported for local repositories, i.e., those with a file:// URI scheme.
hub(x)
: get the value of hub.
hub(x) <- value
: store the value
of hub for x
.
shortLabel(x)
: get the value of hub.
shortLabel(x) <- value
: store the value
of shortLabel for x
.
longLabel(x)
: get the value of hub.
longLabel(x) <- value
: store the value
of longLabel for x
.
genomeFile(x)
: get the value of hub.
genomeFile(x) <- value
: store the value
of genomesFile for x
.
email(x)
: get the value of hub.
email(x) <- value
: store the value
of email for x
.
descriptionUrl(x)
: get the value of hub.
descriptionUrl(x) <- value
: store the value
of descriptionUrl for x
.
genomeField(x, name, field)
: Get the value
of field
for name
genome.
genomeField(x, name, field) <- value
: Set or Update the field
and value
for name
genome.
genomeInfo(x, name)
: Get the Genome
object for name
genome.
genomeInfo(x) <- value
: Add value
(Genome object) to existing genomes list.
Genome
takes named arguemnts of all UCSC supported fields for genome
file(like genome, trackDb, twoBitPath
, etc).
Michael Lawrence
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | th <- TrackHub(system.file("tests", "trackhub", package = "rtracklayer"))
uri(th)
genome(th)
length(th)
th$hg19
th[["hg19"]]
hub(th)
email(th)
## Not run:
hub(th) <- "new_hub"
writeTrackHub(th)
## End(Not run)
|
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