CoreillCNV_UCSC: Create one track of the genomic positions of CNV in...

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 CNV in chromosomal aberration and inherited disorders from the NIGMS Human Genetic Cell Repository data

Description

Create one track of the genomic positions of copy-number variants (CNVs) in chromosomal aberration and inherited disorder cell lines from the NIGMS Human Genetic Cell Repository using the Gviz bioconductor package.

Usage

CoreillCNV_UCSC(gen, chr, start, end,title="Coriell CNVs", showId=FALSE)

Arguments

gen	the name of the genome. Data is not currently available for GRCh38 (hg38).
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)
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://bioconductor.org/packages/release/bioc/html/Gviz.html

http://genome-euro.ucsc.edu/cgi-bin/hgTrackUi?hgsid=202839739_2hYQ1BAOuBMAR620GjrtdrFAy6dn&c=chr6&g=coriellDelDup

See Also

snpLocations_UCSC, structureBiomart_ENSEMBL, snpBiomart_ENSEMBL, COSMIC_UCSC, ClinVarMain_UCSC, ClinVarCnv_UCSC

Examples

library("Gviz")
gen <- "hg19"
chrom <- "chr2"
start <- 38290160
end <- 38303219

if(interactive()){
    coreilVariant<-CoreillCNV_UCSC(gen,chrom,start,end)
    plotTracks(coreilVariant, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
} else {
     data(coreilVarianttrack)
    plotTracks(coreilVariant, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}

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