coMET (version 1.4.4)

knownGenes_UCSC: 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, 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)

showId

Show the ID of the genetic elements

Value

An UcscTrack object of Gviz

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)
}else {
  data(genesUcsctrack)
  plotTracks(genesUcsctrack, from = start, to =end)
}