GWAScatalog_UCSC {coMET} | R Documentation

## 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)
    } else {
      data(GWASTrack)
      plotTracks(gwastrack, from = start, to =end)
    }

[Package coMET version 1.26.0 Index]