makeFeatureDbFromUCSC: Making a FeatureDb object from annotations available at the UCSC Genome Browser

Description

The 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.

Usage

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)

Arguments

genome

genome abbreviation used by UCSC and obtained by ucscGenomes()[ , "db"]. For example: "hg18".

track

name of the UCSC track. Use supportedUCSCFeatureDbTracks to get the list of available tracks for a particular genome

tablename

name of the UCSC table containing the annotations to retrieve. Use the supportedUCSCFeatureDbTables utility function to get the list of supported tables for a track.

columns

a named character vector to list out the names and types of the other columns that the downloaded track should have. Use UCSCFeatureDbTableSchema to retrieve this information for a particular table.

url,goldenPath_url

use to specify the location of an alternate UCSC Genome Browser.

chromCol

If the schema comes back and the 'chrom' column has been labeled something other than 'chrom', use this argument to indicate what that column has been labeled as so we can properly designate it. This could happen (for example) with the knownGene track tables, which has no 'chromStart' or 'chromEnd' columns, but which DOES have columns that could reasonably substitute for these columns under particular circumstances. Therefore we allow these three columns to have arguments so that their definition can be re-specified

chromStartCol

Same thing as chromCol, but for renames of 'chromStart'

chromEndCol

Same thing as chromCol, but for renames of 'chromEnd'

taxonomyId

By default this value is NA and the organism inferred will be used to look up the correct value for this. But you can use this argument to override that and supply your own valid taxId here.

Value

FeatureDb object for makeFeatureDbFromUCSC. Or in the case of supportedUCSCFeatureDbTracks and UCSCFeatureDbTableSchema a named character vector

Details

makeFeatureDbFromUCSC 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.

Examples

Run this code

## 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