Creation of an UCSC's DNase clusters track

Description

Creation of DNase cluster track from a connection to UCSC genome browser in using the GViz bioconductor package

Usage

DNAse_UCSC(gen, chr, start, end, mySession, track.name = "DNase Clusters", table.name = NULL)

Arguments

Value

An AnnotationTrack 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=wgEncodeDNAseSuper

Examples

library("Gviz")
library("rtracklayer")

gen <- "hg19"
chr <- "chr7"
start <- 38290160
end <- 38303219
if(interactive()){
  BROWSER.SESSION="UCSC"
  mySession <- browserSession(BROWSER.SESSION)
  genome(mySession) <- gen
  track.name="Broad ChromHMM"
  tablestrack<-tableNames(ucscTableQuery(mySession, track=track.name))
  table.name<-tablestrack[1]
  dnasetrack<-DNAse_UCSC(gen,chr,start,end,mySession)
  plotTracks(dnasetrack, from = start, to =end)
}else {
    data(dnasetrack)
   plotTracks(dnasetrack, from = start, to =end)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(coMET)
Loading required package: grid
Loading required package: biomaRt
Loading required package: Gviz
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: psych

Attaching package: 'psych'

The following object is masked from 'package:IRanges':

    reflect

Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/coMET/DNAse_UCSC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DNAse_UCSC
> ### Title: Creation of an UCSC's DNase clusters track
> ### Aliases: DNAse_UCSC
> ### Keywords: hplot
> 
> ### ** Examples
> 
> library("Gviz")
> library("rtracklayer")
> 
> gen <- "hg19"
> chr <- "chr7"
> start <- 38290160
> end <- 38303219
> #if(interactive()){
>   BROWSER.SESSION="UCSC"
>   mySession <- browserSession(BROWSER.SESSION)
>   genome(mySession) <- gen
Error in `genome<-`(`*tmp*`, value = "hg19") : 
  Failed to set session genome to 'hg19'
Calls: genome<- -> genome<-
Execution halted