coMET (version 1.2.0)

snpBiomart: Create a short variation track from ENSEMBL

Description

Create a 'Short Variation' track from ENSEMBL using the Gviz bioconductor package

Usage

snpBiomart(chr, start, end, dataset, showId=FALSE, title = NULL)

Arguments

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)

dataset

The name of the database. Example "hsapiens_snp_som"

showId

Show the the ID of element or not

title

The name of the annotation track

Value

An AnnotationTrack object of Gviz

References

Go to ENSEMBL Biomart

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

See Also

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

Examples

library("Gviz")
gen <- "hg19"
chr <- "chr2"
start <- 38290160
end <- 38303219

if(interactive()){
  snptrack <- snpBiomart(chr, start, end, 
                       dataset="hsapiens_snp_som",showId=FALSE)
  plotTracks(snptrack, from=start, to=end) 
} else {
  data(snpBiomarttrack)
  plotTracks(snptrack, from=start, to=end)
}