rtracklayer: UCSCSchema-class – R documentation

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UCSCSchema-class

UCSC Schema

Description

This is a preliminary class that describes a table in the UCSC database. The description includes the table name, corresponding genome, row count, and a textual description of the format. In the future, we could provide more table information, like the links and sample data frame. This is awaiting a use-case.

Accessor methods

In the code snippets below, x/object is a UCSCSchema object.

: genome(x): Get the genome for the table.
: tableName(x): Get the name of the table.
: nrow(x): Get the number of rows in the table.
: formatDescription(x): Get a textual description of the table format.

Author(s)

Michael Lawrence

Examples

## Not run: 
session <- browserSession()
genome(session) <- "mm9"
query <- ucscTableQuery(session, "knownGene")
schema <- ucscSchema(query)
nrow(schema)

## End(Not run)

rtracklayer

R interface to genome annotation files and the UCSC genome browser

v1.50.0

Artistic-2.0 + file LICENSE

Authors

Michael Lawrence, Vince Carey, Robert Gentleman

Initial release