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

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

Description

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

Usage

genes_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, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

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)
}

TiphaineCMartin/coMET_original documentation built on May 9, 2019, 4:49 p.m.