rtracklayer (version 1.32.0)

UCSCTableQuery-class: Querying UCSC Tables

Description

The UCSC genome browser is backed by a large database, which is exposed by the Table Browser web interface. Tracks are stored as tables, so this is also the mechanism for retrieving tracks. The UCSCTableQuery class represents a query against the Table Browser. Storing the query fields in a formal class facilitates incremental construction and adjustment of a query.

Details

There are five supported fields for a table query: [object Object],[object Object],[object Object],[object Object],[object Object]

A common workflow for querying the UCSC database is to create an instance of UCSCTableQuery using the ucscTableQuery constructor, invoke tableNames to list the available tables for a track, and finally to retrieve the desired table either as a data.frame via getTable or as a track via track. See the examples.

The reason for a formal query class is to facilitate multiple queries when the differences between the queries are small. For example, one might want to query multiple tables within the track and/or same genomic region, or query the same table for multiple regions. The UCSCTableQuery instance can be incrementally adjusted for each new query. Some caching is also performed, which enhances performance.

Examples

session <- browserSession()
genome(session) <- "mm9"
trackNames(session) ## list the track names
## choose the Conservation track for a portion of mm9 chr1
query <- ucscTableQuery(session, "Conservation",
                        GRangesForUCSCGenome("mm9", "chr12",
                                             IRanges(57795963, 57815592)))
## list the table names
tableNames(query)
## get the phastCons30way track
tableName(query) <- "phastCons30way"
## retrieve the track data
track(query)  # a GRanges object
## get a data.frame summarizing the multiple alignment
tableName(query) <- "multiz30waySummary"
getTable(query)

genome(session) <- "hg18"
query <- ucscTableQuery(session, "snp129",
                        names = c("rs10003974", "rs10087355", "rs10075230"))
ucscSchema(query)
getTable(query)