ensembldb (version 1.4.6)

getGeneRegionTrackForGviz: Utility functions

Description

Utility functions integrating EnsDb objects with other Bioconductor packages.

Usage

## S3 method for class 'EnsDb':
getGeneRegionTrackForGviz(x, filter=list(),
                                            chromosome=NULL,
                                            start=NULL, end=NULL,
                                            featureIs="gene_biotype")

Arguments

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 object extending BasicFilter or a list of such object(s) to select specific entries from the database (see examples below).

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.

Value

• For getGeneRegionTrackForGviz: see method description above.

See Also

BasicFilter transcripts

Examples

library(EnsDb.Hsapiens.v75)
edb <- EnsDb.Hsapiens.v75
######   getGeneRegionTrackForGviz
##
## Get all genes encoded on chromosome Y in the specifyed region.
AllY <- getGeneRegionTrackForGviz(edb, chromosome="Y", start=5000000,
                                  end=7000000)
## We could plot this now using plotTracks(GeneRegionTrack(AllY))

## We can also use filters to further restrict the query to e.g.
## all lincRNA genes encoded in that region.
lincsY <- getGeneRegionTrackForGviz(edb, chromosome="Y", start=5000000,
                                    end=7000000,
                                    filter=GenebiotypeFilter("lincRNA"))