structureBiomart_ENSEMBL: Create a structural variation track from ENSEMBL

In TiphaineCMartin/coMET: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

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 = "Structural variation")

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	The name of the annotation track

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

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,
                                   fontfamily="sans",fontfamily.title="sans")
}else {
  data(strucBiomarttrack)
  plotTracks(strutrack, from=start, to=end,
                                   fontfamily="sans",fontfamily.title="sans")
}

TiphaineCMartin/coMET documentation built on April 27, 2022, 6:45 a.m.