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

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/BiofeatureGraphics.R

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

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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

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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)
}

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