coMET (version 1.4.4)

GWAScatalog_UCSC: Create one track of the genomic positions of variants from the GWAS catalog

Description

Create one track of the genomic positions of variants from the NHGRI Catalog of Published Genome-Wide Association Studies using the Gviz bioconductor package

Usage

GWAScatalog_UCSC(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

An UcscTrack object of Gviz

References

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

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

See Also

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

Examples

library("Gviz")
gen <- "hg38"
chrom <- "chr2"
start <- 10000
end <- 100000

if(interactive()) {
  gwastrack <-GWAScatalog_UCSC(gen,chrom,start,end)
  plotTracks(gwastrack, from = start, to =end)
} else {
  data(GWASTrack)
  plotTracks(gwastrack, from = start, to =end)
}