ClinVarCnv_UCSC: Create one track of the genomic positions of variants from...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/BiofeatureGraphics.R

Description

Create one track of the genomic positions of variants from the ClinVar database (CNV only, Variants excluded) using the Gviz bioconductor package

Usage

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ClinVarCnv_UCSC(gen, chr, start, end, title="ClinVar Variants", showId = FALSE)

Arguments

gen

the name of the genome

chr

the chromosome of interest

start

the first position in region of interest (the smallest value)

end

the last position in region of interest (the biggest value)

title

The name of the annotation track

showId

Show the ID of the genetic elements

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=clinvar

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

See Also

snpLocations_UCSC, structureBiomart_ENSEMBL, snpBiomart_ENSEMBL, CoreillCNV_UCSC, COSMIC_UCSC, ClinVarMain_UCSC

Examples

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library("Gviz")
chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg38"
if(interactive()){
    clinCNV<-ClinVarCnv_UCSC(gen,chrom,start,end)
    plotTracks(clinCNV, from = start, to =end)
}else {
    data(ClinVarCnvTrack)
    plotTracks(clinCNV, from = start, to =end)
}

coMET documentation built on Nov. 1, 2018, 2:17 a.m.