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

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

Description

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

Usage

refGenes_UCSC(gen, chr, start, end, title="Ref Genes UCSC", track = "refGene",
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)
title	Name of tracks
track	the name of table in UCSC for the group "Genes and Gene Prediction"
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

Author(s)

Tiphaine Martin

Tom Hardiman

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"
track <- "refGene"

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

coMET documentation built on Nov. 8, 2020, 5 p.m.