GWAScatalog_UCSC: Create one track of the genomic positions of variants from...

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

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, title="GWAS Catalog", 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)
title	The name of the annotation track
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=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,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(GWASTrack)
  plotTracks(gwastrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}

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