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makeFeatureDbFromUCSC
function allows the user
to make a FeatureDb object from simple annotation tracks at
UCSC. The tracks in question must (at a minimum) have a start, end and
a chromosome affiliation in order to be made into a FeatureDb.
This function requires a precise declaration of its first three
arguments to indicate which genome, track and table wish to be
imported. There are discovery functions provided to make this process
go smoothly.
supportedUCSCFeatureDbTracks(genome)
supportedUCSCFeatureDbTables(genome, track)
UCSCFeatureDbTableSchema(genome, track, tablename)
makeFeatureDbFromUCSC( genome, track, tablename, columns = UCSCFeatureDbTableSchema(genome,track,tablename), url="http://genome.ucsc.edu/cgi-bin/", goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath", chromCol, chromStartCol, chromEndCol, taxonomyId=NA)
ucscGenomes()[ , "db"]
.
For example: "hg18"
.supportedUCSCFeatureDbTracks
to get the list of available
tracks for a particular genomesupportedUCSCFeatureDbTables
utility
function to get the list of supported tables for a track.UCSCFeatureDbTableSchema
to retrieve this
information for a particular table.makeFeatureDbFromUCSC
. Or in
the case of supportedUCSCFeatureDbTracks
and
UCSCFeatureDbTableSchema
a named character vectormakeFeatureDbFromUCSC
is a convenience function that builds a
tiny database from one of the UCSC track tables.
supportedUCSCFeatureDbTracks
a convenience function that
returns potential track names that could be used to make
FeatureDb objects
supportedUCSCFeatureDbTables
a convenience function that
returns potential table names for FeatureDb objects (table names
go with a track name)
UCSCFeatureDbTableSchema
A convenience function that creates a
named vector of types for all the fields that can potentially be
supported for a given track. By default, this will be called on
your specified tablename to include all of the fields in a track.
ucscGenomes
,
## Display the list of genomes available at UCSC:
library(GenomicFeatures)
library(rtracklayer)
ucscGenomes()[ , "db"]
## Display the list of Tracks supported by makeFeatureDbFromUCSC():
# supportedUCSCFeatureDbTracks("mm10")
## Display the list of tables supported by your track:
supportedUCSCFeatureDbTables(genome="mm10",
track="qPCR Primers")
## Display fields that could be passed in to colnames:
UCSCFeatureDbTableSchema(genome="mm10",
track="qPCR Primers",
tablename="qPcrPrimers")
## Retrieving a full transcript dataset for Mouse from UCSC:
fdb <- makeFeatureDbFromUCSC(genome="mm10",
track="qPCR Primers",
tablename="qPcrPrimers")
fdb
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