Utility functions

Utility functions integrating EnsDb objects with other Bioconductor packages.

# S4 method for EnsDb
getGeneRegionTrackForGviz(x,
        filter = AnnotationFilterList(), chromosome = NULL,
        start = NULL, end = NULL, featureIs = "gene_biotype")

Arguments

(In alphabetic order)

chromosome

For getGeneRegionTrackForGviz: optional chromosome name to restrict the returned entry to a specific chromosome.

end

For getGeneRegionTrackForGviz: optional chromosomal end coordinate specifying, together with start, the chromosomal region from which features should be retrieved.

featureIs

For getGeneRegionTrackForGviz: whether the gene ("gene_biotype") or the transcript biotype ("tx_biotype") should be returned in column "feature".

filter

A filter describing which results to retrieve from the database. Can be a single object extending AnnotationFilter, an AnnotationFilterList object combining several such objects or a formula representing a filter expression (see examples below or AnnotationFilter for more details).

start

For getGeneRegionTrackForGviz: optional chromosomal start coordinate specifying, together with end, the chromosomal region from which features should be retrieved.

x

For toSAF a GRangesList object. For all other methods an EnsDb instance.

Methods and Functions

getGeneRegionTrackForGviz

Retrieve a GRanges object with transcript features from the EnsDb that can be used directly in the Gviz package to create a GeneRegionTrack. Using the filter, chromosome, start and end arguments it is possible to fetch specific features (e.g. lincRNAs) from the database.

If chromosome, start and end is provided the function internally first retrieves all transcripts that have an exon or an intron in the specified chromosomal region and subsequently fetch all of these transcripts. This ensures that all transcripts of the region are returned, even those that have only an intron in the region.

The function returns a GRanges object with additional annotation columns "feature", "gene", "exon", "exon_rank", "trancript", "symbol" specifying the feature type (either gene or transcript biotype), the (Ensembl) gene ID, the exon ID, the rank/index of the exon in the transcript, the transcript ID and the gene symbol/name.

Value

For getGeneRegionTrackForGviz: see method description above.

Author

Johannes Rainer

See also

transcripts

Examples

library(EnsDb.Hsapiens.v86)
edb <- EnsDb.Hsapiens.v86
######   getGeneRegionTrackForGviz
##
## Get all genes encoded on chromosome Y in the specifyed region.
AllY <- getGeneRegionTrackForGviz(edb, chromosome = "Y", start = 5131959,
                                  end = 7131959)
## We could plot this now using plotTracks(GeneRegionTrack(AllY))