COSMIC_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

[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

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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

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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)
}else {
    data(cosmicVarianttrack)
    plotTracks(cosmicVariant, from = start, to =end)
}

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