coMET (version 1.2.0)

ISCATrack: Create one track of the genomic positions of variants from ISCA

Description

Create one track of the genomic positions of variants from International Standards for Cytogenomic Arrays (ISCA) Consortium using the Gviz bioconductor package

Usage

ISCATrack(gen, chr, start, end, mySession, table.name, showId=FALSE)

Arguments

gen

the name of the genome

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)

mySession

the object session from the function browserSession of rtracklayer

table.name

A table of ISCAT classifications: iscaBenign, iscaCuratedBenign, iscaCuratedPathogenic, iscaLikelyBenign, iscaLikelyPathogenic, iscaPathGainCum, iscaPathLossCum, iscaPathogenic, iscaUncertain

showId

Show the ID of the genetic elements

Value

An UcscTrack object of Gviz

References

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

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

See Also

GWASTrack, knownGenesUCSC, genesNameENSEMBL, GeneReviewsTrack, GADTrack, genesENSEMBL, xenorefGenesUCSC, transcriptENSEMBL,

Examples

library("Gviz")
gen <- "hg19"
chr <- "chr2"
start <- 38292433
end <- 38305492

if(interactive()){
  BROWSER.SESSION="UCSC"
  mySession <- browserSession(BROWSER.SESSION)
  genome(mySession) <- gen
  iscatrack <-ISCATrack(gen,chrom,start,end,mySession, table="iscaPathogenic")
  plotTracks(iscatrack, from = start, to =end)
} else {
  data(ISCAtrack)
  plotTracks(iscatrack, from = start, to =end)
}