R Graphical Manual

Last data update: 2014.03.03

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select (Package: ensembldb) : Integration into the AnnotationDbi framework

Several of the methods available for AnnotationDbi objects are also implemented for EnsDb objects. This enables to extract data from EnsDb objects in a similar fashion than from objects inheriting from the base annotation package class AnnotationDbi. In addition to the standard usage, the select and mapIds for EnsDb objects support also the filter framework of the ensembdb package and thus allow to perform more fine-grained queries to retrieve data.

● Data Source: BioConductor
● Keywords: classes
● Alias: columns,EnsDb-method, keys,EnsDb-method, keytypes,EnsDb-method, mapIds,EnsDb-method, select, select,EnsDb-method
● 0 images

EnsDb-class (Package: ensembldb) : Basic usage of an Ensembl based annotation database

Get some basic information from an Ensembl based annotation package generated with makeEnsembldbPackage.

● Data Source: BioConductor
● Keywords: classes
● Alias: EnsDb, EnsDb-class, buildQuery, buildQuery,EnsDb-method, dbconn, dbconn,EnsDb-method, ensemblVersion, ensemblVersion,EnsDb-method, listColumns, listColumns,EnsDb-method, listGenebiotypes, listGenebiotypes,EnsDb-method, listTables, listTables,EnsDb-method, listTxbiotypes, listTxbiotypes,EnsDb-method, metadata, metadata,EnsDb-method, organism, organism,EnsDb-method, seqinfo, seqinfo,EnsDb-method, seqlevels, seqlevels,EnsDb-method, show, show,EnsDb-method, updateEnsDb, updateEnsDb,EnsDb-method
● 0 images

exonsBy (Package: ensembldb) : Retrieve annotation data from an Ensembl based package

Retrieve gene/transcript/exons annotations stored in an Ensembl based database package generated with the makeEnsembldbPackage function.

● Data Source: BioConductor
● Keywords: classes
● Alias: cdsBy, cdsBy,EnsDb-method, disjointExons,EnsDb-method, exons, exons,EnsDb-method, exonsBy, exonsBy,EnsDb-method, exonsByOverlaps,EnsDb-method, fiveUTRsByTranscript,EnsDb-method, genes, genes,EnsDb-method, promoters, promoters,EnsDb-method, threeUTRsByTranscript,EnsDb-method, toSAF, toSAF,GRangesList-method, transcripts, transcripts,EnsDb-method, transcriptsBy, transcriptsBy,EnsDb-method, transcriptsByOverlaps,EnsDb-method
● 0 images

lengthOf (Package: ensembldb) : Calculating lengths of features

These methods allow to calculate the lengths of features (transcripts, genes, CDS, 3' or 5' UTRs) defined in an EnsDb object or database.

● Data Source: BioConductor
● Keywords: classes
● Alias: lengthOf, lengthOf,EnsDb-method, lengthOf,GRangesList-method
● 0 images

seqlevelsStyle (Package: ensembldb) : Support for other than Ensembl seqlevel style

The methods and functions on this help page allow to integrate EnsDb objects and the annotations they provide with other Bioconductor annotation packages that base on chromosome names (seqlevels) that are different from those defined by Ensembl.

● Data Source: BioConductor
● Keywords: classes
● Alias: seqlevelsStyle, seqlevelsStyle,EnsDb-method, seqlevelsStyle<-, seqlevelsStyle<-,EnsDb-method, supportedSeqlevelsStyles, supportedSeqlevelsStyles,EnsDb-method
● 0 images

getGenomeFaFile (Package: ensembldb) : Functionality related to DNA/RNA sequences

Utility functions related to RNA/DNA sequences, such as extracting RNA/DNA sequences for features defined in Ensb.

● Data Source: BioConductor
● Keywords: classes
● Alias: getGenomeFaFile, getGenomeFaFile,EnsDb-method
● 0 images

getGeneRegionTrackForGviz (Package: ensembldb) : Utility functions

Utility functions integrating EnsDb objects with other Bioconductor packages.

● Data Source: BioConductor
● Keywords: classes
● Alias: getGeneRegionTrackForGviz, getGeneRegionTrackForGviz,EnsDb-method
● 0 images

GeneidFilter-class (Package: ensembldb) : Filter results fetched from the Ensembl database

These classes allow to specify which entries (i.e. genes, transcripts or exons) should be retrieved from the database.

● Data Source: BioConductor
● Keywords: classes
● Alias: BasicFilter-class, EntrezidFilter-class, ExonidFilter-class, ExonrankFilter-class, GRangesFilter-class, GenebiotypeFilter-class, GeneidFilter-class, GenenameFilter-class, SeqendFilter-class, SeqnameFilter-class, SeqstartFilter-class, SeqstrandFilter-class, TxbiotypeFilter-class, TxidFilter-class, column,EntrezidFilter,missing,missing-method, column,ExonidFilter,missing,missing-method, column,ExonrankFilter,missing,missing-method, column,GRangesFilter,missing,missing-method, column,GenebiotypeFilter,missing,missing-method, column,GeneidFilter,missing,missing-method, column,GenenameFilter,missing,missing-method, column,SeqendFilter,missing,missing-method, column,SeqnameFilter,missing,missing-method, column,SeqstartFilter,missing,missing-method, column,SeqstrandFilter,missing,missing-method, column,TxbiotypeFilter,missing,missing-method, column,TxidFilter,missing,missing-method, where,EntrezidFilter,missing,missing-method, where,ExonidFilter,missing,missing-method, where,ExonrankFilter,missing,missing-method, where,GRangesFilter,missing,missing-method, where,GenebiotypeFilter,missing,missing-method, where,GeneidFilter,missing,missing-method, where,GenenameFilter,missing,missing-method, where,SeqendFilter,missing,missing-method, where,SeqnameFilter,missing,missing-method, where,SeqstartFilter,missing,missing-method, where,SeqstrandFilter,missing,missing-method, where,TxbiotypeFilter,missing,missing-method, where,TxidFilter,missing,missing-method
● 1 images

SeqendFilter (Package: ensembldb) :

These functions allow to create filter objects that can be used to retrieve specific elements from the annotation database.

● Data Source: BioConductor
● Keywords: data
● Alias: EntrezidFilter, ExonidFilter, ExonrankFilter, GRangesFilter, GenebiotypeFilter, GeneidFilter, GenenameFilter, SeqendFilter, SeqnameFilter, SeqstartFilter, SeqstrandFilter, TxbiotypeFilter, TxidFilter
● 0 images

makeEnsembldbPackage (Package: ensembldb) :

The functions described on this page allow to build EnsDb annotation objects/databases from Ensembl annotations. The most complete set of annotations, which include also the NCBI Entrezgene identifiers for each gene, can be retrieved by the functions using the Ensembl Perl API (i.e. functions fetchTablesFromEnsembl, makeEnsemblSQLiteFromTables). Alternatively the functions ensDbFromAH, ensDbFromGRanges, ensDbFromGff and ensDbFromGtf can be used to build EnsDb objects using GFF or GTF files from Ensembl, which can be either manually downloaded from the Ensembl ftp server, or directly form within R using AnnotationHub. The generated SQLite database can be packaged into an R package using the makeEnsembldbPackage.

● Data Source: BioConductor
● Keywords: data
● Alias: ensDbFromAH, ensDbFromGRanges, ensDbFromGff, ensDbFromGtf, fetchTablesFromEnsembl, makeEnsemblSQLiteFromTables, makeEnsembldbPackage
● 0 images