FeatureDb-class: FeatureDb objects

In Bioconductor/GenomicFeatures: Query the gene models of a given organism/assembly

FeatureDb objects

Description

WARNING: The FeatureDb/makeFeatureDbFromUCSC/features code base is no longer actively maintained and FeatureDb-related functionalities might get deprecated in the near future. Please use makeFeatureDbFromUCSC for a convenient way to import transcript annotations from UCSC online resources into Bioconductor.

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

Bioconductor/GenomicFeatures documentation built on Nov. 7, 2024, 4:25 a.m.