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

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

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, 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

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

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