HistoneAll_UCSC {coMET} | R Documentation

## Create multiple tracks of histone modifications from the UCSC genome browser

### Description

Create multiple tracks of histone modifications from the UCSC genome browser (ENCODE/Broad) using the Gviz bioconductor package

### Usage

    HistoneAll_UCSC(gen, chr, start, end, mySession, pattern = NULL,
              track.name = "Broad Histone", table.name = NULL)

### 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)
`mySession` | the object session from the function browserSession of rtracklayer
`pattern` | The cell type
`track.name` | the name of the track, for example: "Broad Histone"
`table.name` | the name of the table from the track

### Value

A list of AnnotationTrack object of Gviz

### Author(s)

Tiphaine Martin

### References

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

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

### See Also

`HistoneOne_UCSC`,

### Examples

    library("Gviz")
    library("rtracklayer")
    gen <- "hg19"
    chr <- "chr2"
    start <- 38290160
    end <- 38313219

    if(interactive()){
      BROWSER.SESSION="UCSC"
      mySession <- browserSession(BROWSER.SESSION)
      genome(mySession) <- gen
      pattern1 <- "GM12878"

      histonalltrack<-HistoneAll_UCSC(gen,chr,start,end,mySession,
      pattern=pattern1,track.name="Broad Histone")
      plotTracks(histonalltrack, from = start, to =end)
    } else {
      data(histonalltrack)
      plotTracks(histonalltrack, from = start, to =end)
    }

[Package coMET version 1.24.0 Index]