ISCA_UCSC {coMET} | R Documentation

## 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)
    } else {
      data(ISCAtrack_Grch38)
      plotTracks(iscatrack, from = start, to =end)
    }

[Package coMET version 1.16.0 Index]