UCSCSchema-class: UCSC Schema

In rtracklayer: R interface to genome annotation files and the UCSC genome browser

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 documentation built on Nov. 8, 2020, 6:50 p.m.