R Graphical Manual

Last data update: 2014.03.03

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MultiDb-class (Package: OrganismDbi) : MultiDb and OrganismDb objects

The OrganismDb class is a container for storing knowledge about existing Annotation packages and the relationships between these resources. The purpose of this object and it's associated methods is to provide a means by which users can conveniently query for data from several different annotation resources at the same time using a familiar interface.

● Data Source: BioConductor
● Keywords:
● Alias: MultiDb, MultiDb-class, class:MultiDb
● 0 images

mapToTranscripts (Package: OrganismDbi) : Map range coordinates between transcripts and genome space

Map range coordinates between features in the transcriptome and genome (reference) space.

● Data Source: BioConductor
● Keywords: methods, utilities
● Alias: mapToTranscripts,ANY,MultiDb-method
● 0 images

makeOrganismDbFromBiomart (Package: OrganismDbi) :

The makeOrganismDbFromBiomart function allows the user to make a OrganismDb object from transcript annotations available on a BioMart database. This object has all the benefits of a TxDb, plus an associated OrgDb and GODb object.

● Data Source: BioConductor
● Keywords:
● Alias: makeOrganismDbFromBiomart
● 0 images

makeOrganismDbFromTxDb (Package: OrganismDbi) :

The makeOrganismDbFromTxDb function allows the user to make a OrganismDb object from an existing TxDb object.

● Data Source: BioConductor
● Keywords:
● Alias: makeOrganismDbFromTxDb
● 0 images

makeOrganismDbFromUCSC (Package: OrganismDbi) :

The makeOrganismDbFromUCSC function allows the user to make a OrganismDb object from transcript annotations available at the UCSC Genome Browser.

● Data Source: BioConductor
● Keywords:
● Alias: makeOrganismDbFromUCSC
● 0 images

makeOrganismPackage (Package: OrganismDbi) :

makeOrganismPackage is a method that generates a package that will load an appropriate annotationOrganismDb object that will in turn point to existing annotation packages.

● Data Source: BioConductor
● Keywords:
● Alias: makeOrganismPackage
● 0 images

rangeBasedAccessors (Package: OrganismDbi) :

Generic functions to extract genomic features from an object. This page documents the methods for OrganismDb objects only.

● Data Source: BioConductor
● Keywords: methods
● Alias: cds,MultiDb-method, exons,MultiDb-method, genes,MultiDb-method, transcripts,MultiDb-method
● 0 images