knownGenes_UCSC: Create a track of known genes from the UCSC genome browser

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

Create a track of known genes from the UCSC genome browser

Description

Create a track of known genes from the UCSC genome browser using the Gviz bioconductor package

Usage

knownGenes_UCSC(gen, chr, start, end,title="UCSC known Genes", showId=TRUE)

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)
title	Name of tracks
showId	Show the ID of the genetic elements

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

References

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

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

See Also

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

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr7"
start <- 38290160
end <- 38303219

if(interactive()) {
  genesUcsctrack<-knownGenes_UCSC(gen,chr,start,end,showId=TRUE)
  plotTracks(genesUcsctrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}else {
  data(genesUcsctrack)
  plotTracks(genesUcsctrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}

TiphaineCMartin/coMET documentation built on April 27, 2022, 6:45 a.m.