ClinVarMain_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 (Variants only, CNV excluded) using the Gviz bioconductor package

Usage

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ClinVarMain_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, ClinVarCnv_UCSC

Examples

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library("Gviz")
gen <- "hg38"
chrom <- "chr2"
start <- 100000
end <- 10000000

if(interactive()) {
    clinVariant<-ClinVarMain_UCSC(gen,chrom,start,end)
    plotTracks(clinVariant, from = start, to =end)
}else{
    data(clinVarMaintrack)
    plotTracks(clinVariant, from = start, to =end)
}

coMET documentation built on May 2, 2018, 4:21 a.m.