coMET (version 1.2.0)

snpLocationsUCSC: Create a SNP track from UCSC

Description

Create a SNP track from UCSC using the Gviz bioconductor package

Usage

snpLocationsUCSC(gen, chr, start, end, track)

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)

track

The name of the database. Example "snp138"

Value

An UcscTrack object of Gviz

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

snpLocationsUCSC, structureBiomart, COSMICTrack, CoreillCNVTrack, ClinVarMainTrack, ClinVarCnvTrack,

Examples

library("Gviz")
gen <- "hg19"
chr <- "chr7"
start <- 38290160
end <- 38303219

if(interactive()) {
  snpUCSCtrack<-snpLocationsUCSC(gen,chr,start,end,"snp138")
  plotTracks(snpUCSCtrack, from = start, to =end) 
} else {
  data(snpUCSCtrack)
  plotTracks(snpUCSCtrack, from = start, to =end) 
}