transcript_ENSEMBL: Create a track of transcripts from ENSEMBL

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/BiofeatureGraphics.R

Description

Create a track to visualize different transcripts from ENSEMBL using the Gviz bioconductor package

Usage

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transcript_ENSEMBL(gen, chr, start, end,showId = FALSE)

Arguments

gen

the name of the genome

chr

the chromosome of interest

start

the first position in the region of interest (the smallest value)

end

the last position in the region of interest (the largest value)

showId

Show the ID of the genetic elements

Value

A BiomartGeneRegionTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=ensGene

See Also

ISCA_UCSC, GWAScatalog_UCSC, knownGenes_UCSC, genesName_ENSEMBL, GeneReviews_UCSC, GAD_UCSC, genes_ENSEMBL, xenorefGenes_UCSC,

Examples

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library("Gviz")
gen <- "hg19"
chr <- "chr2"
start <- 32290160
end <- 33303219

if(interactive()){
  transENSMBLtrack<-transcript_ENSEMBL(gen,chr,start,end,showId=TRUE)
  plotTracks(transENSMBLtrack, from=start, to=end)
} else {
  data(transENSMBLtrack)
  plotTracks(transENSMBLtrack, from=start, to=end)
}
 

coMET documentation built on Nov. 23, 2017, 2:05 a.m.