snpLocations_UCSC: Create a SNP track from UCSC

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

Description

Create a SNP track from UCSC using the Gviz bioconductor package

Usage

snpLocations_UCSC(gen, chr, start, end,title= "SNPs UCSC", 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)
title	Name of tracks
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

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. 8, 2020, 5 p.m.