Utility functions

Description

Utility functions integrating EnsDb objects with other Bioconductor packages.

Usage

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

Arguments

(In alphabetic order)

Value

For getGeneRegionTrackForGviz: see method description above.

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.

Author(s)

Johannes Rainer

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"))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(ensembldb)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ensembldb/EnsDb-utils.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getGeneRegionTrackForGviz
> ### Title: Utility functions
> ### Aliases: getGeneRegionTrackForGviz
> ###   getGeneRegionTrackForGviz,EnsDb-method
> ### Keywords: classes
> 
> ### ** 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"))
Warning messages:
1: In getUTRsByTranscript(x = x, what = "five", columns = columns,  :
  No fiveUTR found!
2: In getUTRsByTranscript(x = x, what = "three", columns = columns,  :
  No threeUTR found!
3: In .local(x, by, ...) : No cds found!
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>