repeatMasker_UCSC {coMET} | R Documentation

## Create one track of the genomic positions of regions from repeatMasker_UCSC

### Description

Create one track of the genomic positions of regions from repeatMasker_UCSC using the Gviz bioconductor package

### Usage

    repeatMasker_UCSC(gen, chr, start, end, title="RepeatMasker",
    showId=FALSE,type_stacking="full")

### 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)
`title` | The name of the annotation track
`showId` | Show the ID of the genetic elements
`type_stacking` | the type of stacking data for this track. More information go to Gviz (the option "stacking")

### Value

An UcscTrack object of Gviz

### Author(s)

Tiphaine Martin

### References

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

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

### Examples

    library("Gviz")
    gen <- "hg38"
    chr <- "chr2"
    start <- 38290160
    end <- 38303219

    if(interactive()){
      rmtrack <-repeatMasker_UCSC(gen,chr,start,end,showId=TRUE)
      plotTracks(rmtrack, from = start, to = end)
    } else {
      data(repeatMaskerTrack)
      plotTracks(rmtrack, from = start, to = end)
    }

[Package coMET version 1.24.0 Index]