coMET (version 1.4.4)

structureBiomart_ENSEMBL: Create a structural variation track from ENSEMBL

Description

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

Usage

structureBiomart_ENSEMBL(gen, chr, start, end, strand, dataset, showId=FALSE, title_track = NULL)

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)

strand

the strand to extract structure data for

dataset

The name of the database. Example "hsapiens_structvar_som"

showId

Show the the ID of the element

title_track

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

snpLocations_UCSC, snpBiomart_ENSEMBL, COSMIC_UCSC, CoreillCNV_UCSC, ClinVarMain_UCSC, ClinVarCnv_UCSC,

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr2"
start <- 38290160
end <- 38303219

if(interactive()){
  strutrack <- structureBiomart_ENSEMBL(chr, start, end,
                              strand, dataset="hsapiens_structvar_som")
  plotTracks(strutrack, from=start, to=end)
}else {
  data(strucBiomarttrack)
  plotTracks(strutrack, from=start, to=end)
}