coMET (version 1.4.4)

ClinVarMain_UCSC: Create one track of the genomic positions of variants from the ClinVar database (variants only)

Description

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

Usage

ClinVarMain_UCSC(gen, chr, start, end, 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)

showId

Show the ID of the genetic elements

Value

An UcscTrack object of Gviz

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

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)
}