ISCA_UCSC: Create one track of the genomic positions of variants from...

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

Create one track of the genomic positions of variants from ISCA [obselete database]

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

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

# 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,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(ISCAtrack_Grch38)
  plotTracks(iscatrack, from = start, to =end,
                                   fontfamily="sans",fontfamily.title="sans")
}

TiphaineCMartin/coMET documentation built on April 27, 2022, 6:45 a.m.