COSMIC_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 COSMIC [obselete]

Description

[obselete] No more possible to extract COSMIC data from UCSC.

Create one track of the genomic positions of variants from COSMIC, the "Catalogue Of Somatic Mutations In Cancer" in extracting data from UCSC and using the Gviz bioconductor package.

Usage

COSMIC_UCSC(gen, chr, start, end,title= "COSMIC", 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=cosmic

See Also

snpLocations_UCSC, structureBiomart_ENSEMBL, snpBiomart_ENSEMBL, CoreillCNV_UCSC, ClinVarMain_UCSC, ClinVarCnv_UCSC,

Examples

library("Gviz")
chrom <- "chr2"
start <- 38290160
end <- 38303219
gen <- "hg19"
if(interactive()){
    cosmicVariant<-COSMIC_UCSC(gen,chrom,start,end)
    plotTracks(cosmicVariant, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}else {
    data(cosmicVarianttrack)
    plotTracks(cosmicVariant, from = start, to =end,
    fontfamily="sans",fontfamily.title="sans")
}

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