snpLocations_UCSC {coMET} | R Documentation

## Create a SNP track from UCSC

### Description

Create a SNP track from UCSC using the Gviz bioconductor package

### Usage

    snpLocations_UCSC(gen, chr, start, end,title= "SNPs UCSC", track="All SNPs(142)")

### 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` | Name of tracks
`track` | The name of the database. Default "All SNPs(142)"

### 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=snp141

http://bioconductor.org/packages/release/bioc/html/Gviz.html

### See Also

`snpLocations_UCSC`, `structureBiomart_ENSEMBL`, `COSMIC_UCSC`, `CoreillCNV_UCSC`, `ClinVarMain_UCSC`, `ClinVarCnv_UCSC`,

### Examples

    library("Gviz")
    gen <- "hg38"
    chr <- "chr7"
    start <- 38290160
    end <- 38303219

    if(interactive()) {
      snpUCSCtrack<-snpLocations_UCSC(gen,chr,start,end,"All SNPs(142)")
      plotTracks(snpUCSCtrack, from = start, to =end)
    } else {
      data(snpUCSCtrack)
      plotTracks(snpUCSCtrack, from = start, to =end)
    }

[Package coMET version 1.26.0 Index]