GWAScatalog_UCSC {coMET} | R Documentation |
Create one track of the genomic positions of variants from the NHGRI Catalog of Published Genome-Wide Association Studies using the Gviz bioconductor package
GWAScatalog_UCSC(gen, chr, start, end, title="GWAS Catalog", showId=FALSE)
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 |
An UcscTrack object of Gviz
Tiphaine Martin
http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=gwasCatalog
http://bioconductor.org/packages/release/bioc/html/Gviz.html
ISCA_UCSC
, knownGenes_UCSC
, genesName_ENSEMBL
,
GeneReviews_UCSC
, GAD_UCSC
, genes_ENSEMBL
, xenorefGenes_UCSC
, transcript_ENSEMBL
,
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) }