ISCA_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

Create one track of the genomic positions of variants from International Standards for Cytogenomic Arrays (ISCA) Consortium using the Gviz bioconductor package (obselete datbase, Impossible to access to data from UCSC from September 2015)

Usage

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ISCA_UCSC(gen, chr, start, end, mySession, table.name,title="ISCA", 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

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://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

GWAScatalog_UCSC, knownGenes_UCSC, genesName_ENSEMBL, GeneReviews_UCSC, GAD_UCSC, genes_ENSEMBL, xenorefGenes_UCSC, transcript_ENSEMBL,

Examples

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# Oboselet function

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

if(interactive()){
  BROWSER.SESSION="UCSC"
  mySession <- browserSession(BROWSER.SESSION)
  genome(mySession) <- gen
  iscatrack <-ISCA_UCSC(gen,chrom,start,end,mySession,title="ISCA", table="iscaPathogenic")
  plotTracks(iscatrack, from = start, to =end)
} else {
  data(ISCAtrack_Grch38)
  plotTracks(iscatrack, from = start, to =end)
}

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