FeatureDb-class: FeatureDb objects

In jmacdon/GenomicFeatures: Conveniently import and query gene models

Description

The FeatureDb class is a generic container for storing genomic locations of an arbitrary type of genomic features.

See ?TxDb for a container for storing transcript annotations.

See ?makeFeatureDbFromUCSC for a convenient way to make FeatureDb objects from BioMart online resources.

Methods

In the code snippets below, x is a FeatureDb object.

metadata(x): Return x's metadata in a data frame.

Author(s)

Marc Carlson

See Also

• The TxDb class for storing transcript annotations.

• makeFeatureDbFromUCSC for a convenient way to make a FeatureDb object from UCSC online resources.

• saveDb and loadDb for saving and loading the database content of a FeatureDb object.

• features for how to extract genomic features from a FeatureDb object.

Examples

fdb_file <- system.file("extdata", "FeatureDb.sqlite",
                        package="GenomicFeatures")
fdb <- loadDb(fdb_file)
fdb

jmacdon/GenomicFeatures documentation built on Jan. 2, 2022, 7:40 a.m.