snpLocations_UCSC: Create a SNP track from UCSC

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/BiofeatureGraphics.R

Description

Create a SNP track from UCSC using the Gviz bioconductor package

Usage

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snpLocations_UCSC(gen, chr, start, end, track="All SNPs(142)")

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)

track

The name of the database. Default "All SNPs(142)"

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=snp141

http://bioconductor.org/packages/release/bioc/html/Gviz.html

See Also

snpLocations_UCSC, structureBiomart_ENSEMBL, COSMIC_UCSC, CoreillCNV_UCSC, ClinVarMain_UCSC, ClinVarCnv_UCSC,

Examples

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library("Gviz")
gen <- "hg38"
chr <- "chr7"
start <- 38290160
end <- 38303219

if(interactive()) {
  snpUCSCtrack<-snpLocations_UCSC(gen,chr,start,end,"All SNPs(142)")
  plotTracks(snpUCSCtrack, from = start, to =end)
} else {
  data(snpUCSCtrack)
  plotTracks(snpUCSCtrack, from = start, to =end)
}

coMET documentation built on Nov. 23, 2017, 2:05 a.m.