genes_ENSEMBL: Create one track of the genes in the genomic regions of...

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

View source: R/BiofeatureGraphics.R

Description

Create one track of the genes in the genomic regions of interest from EMSEMBL using the Gviz bioconductor package

Usage

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genes_ENSEMBL(gen, chr, start, end, showId=FALSE,title="genes (ENSEMBL)")

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

title

Name of tracks

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, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

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library("Gviz")
gen <- "hg19"
chrom <- "chr2"
start <- 38290160
end <- 38303219
if(interactive()) {
  genetrack <-genes_ENSEMBL(gen,chrom,start,end,showId=TRUE)
  plotTracks(genetrack, from = start, to =end)
} else {
  data(geneENSEMBLtrack)
  plotTracks(genetrack, from = start, to =end)
}

coMET documentation built on Nov. 1, 2018, 2:17 a.m.