transcript_ENSEMBL: Create a track of transcripts from ENSEMBL

In coMET: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

Description

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

Usage

transcript_ENSEMBL(gen, chr, start, end,showId = FALSE, title="transcripts 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, genes_ENSEMBL, xenorefGenes_UCSC,

Examples

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. 8, 2020, 5 p.m.