coMET (version 1.4.4)

refGenes_UCSC: Create a track of RefSeq genes from the UCSC genome browser

Description

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

Usage

refGenes_UCSC(gen, chr, start, end, IdType="Ref", 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)

IdType

When set to 'ref' shows the gene reference, when set to "name" shows the gene name

showId

Shows the ID or name 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, knownGenes_UCSC

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr7"
start <- 38203219
end <- 38303219
IdType <- "name"

if(interactive()) {
  genesUcsctrack<-refGenes_UCSC(gen,chr,start,end,IdType)
  plotTracks(genesUcsctrack, from = start, to =end)
}else {
  data(genesUcsctrack)
  plotTracks(genesUcsctrack, from = start, to =end)
}