Create a track of RefSeq genes from the UCSC genome browser

Description

Create a track of RefSeq genes from the UCSC genome browser using the Gviz bioconductor package

Usage

refGenes_UCSC(gen, chr, start, end, IdType="Ref", showId=TRUE)

Arguments

Value

An UcscTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

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

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

See Also

ISCA_UCSC, GWAScatalog_UCSC, genesName_ENSEMBL, GeneReviews_UCSC, GAD_UCSC, genes_ENSEMBL, xenorefGenes_UCSC, transcript_ENSEMBL, knownGenes_UCSC

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr7"
start <- 38203219
end <- 38303219
IdType <- "name"

if(interactive()) {
  genesUcsctrack<-refGenes_UCSC(gen,chr,start,end,IdType)
  plotTracks(genesUcsctrack, from = start, to =end)
}else {
  data(genesUcsctrack)
  plotTracks(genesUcsctrack, 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/refGenes_UCSC.Rd_%03d_medium.png", width=480, height=480)
> ### Name: refGenes_UCSC
> ### Title: Create a track of RefSeq genes from the UCSC genome browser
> ### Aliases: refGenes_UCSC
> ### Keywords: hplot
> 
> ### ** Examples
> 
> library("Gviz")
> gen <- "hg38"
> chr <- "chr7"
> start <- 38203219
> end <- 38303219
> IdType <- "name"
> 
> #if(interactive()) {
>   genesUcsctrack<-refGenes_UCSC(gen,chr,start,end,IdType)
>   plotTracks(genesUcsctrack, from = start, to =end)
> }else {
Error: unexpected '}' in "}"
Execution halted