GAD_UCSC {coMET} | R Documentation

## Create one track of the genomic positions of variants from the Genetic Association Database (GAD)

### Description

Create one track of the genomic positions of variants from the Genetic Association Database (GAD) (archive of human genetic association studies of complex diseases and disorders) using the Gviz bioconductor package

### Usage

    GAD_UCSC(gen, chr, start, end,title="GAD", showId=FALSE)

### Arguments

`gen` | the name of the genome. Data is not currently available for GRCh38 (hg38).
`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://bioconductor.org/packages/release/bioc/html/Gviz.html

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

### See Also

`ISCA_UCSC`, `GWAScatalog_UCSC`, `knownGenes_UCSC`, `genesName_ENSEMBL`, `GeneReviews_UCSC`, `genes_ENSEMBL`, `xenorefGenes_UCSC`, `transcript_ENSEMBL`,

### Examples

    library("Gviz")
    gen2 <- "hg19"
    chrom2 <- "chr2"
    start2 <- 38290160
    end2 <- 38303219

    if(interactive()) {
      gadtrack<-GAD_UCSC(gen=gen2 ,chr=chrom2 ,start=start2 ,end=end2)
      plotTracks(gadtrack, from = start2, to =end2)
    } else {
      data(gadtrack)
       plotTracks(gadtrack, from = start2, to =end2)
    }

[Package coMET version 1.16.0 Index]