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Last data update: 2014.03.03

R: Creates a binding motif track from ENSEMBL

bindingMotifsBiomart_ENSEMBL

R Documentation

Creates a binding motif track from ENSEMBL

Description

Creates a binding motif track from ENSEMBL using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

bindingMotifsBiomart_ENSEMBL(gen, chr, start, end, featureDisplay="all", datasetEnsembl = NULL)

Arguments

`gen`	The name of the genome. Currently only handles human data from either the previous version, GRCh37 (also known as hg19) or the current version, GRCh38 (also known as hg38).
`chr`	The chromosome of interest
`start`	The starting position in the region of interest (the smallest value)
`end`	The end position in the region of interest (the largest value)
`featureDisplay`	A vector of regulatory features to be displayed, such as Egr1. Spelling and capitalisation of features must be identical to those in the user guide. There are three possibilities. First, the visualisation of only one feature (e.g. featureDisplay <- "CTCF"), only the name of the specific feature is required. Second, visualisation of a set of features, for this a vector of features is required (e.g. featureDisplay <- c("Egr1","CTCF")). Finally, visualison all features in the genomic region, achived by using the word "all" (e.g. featureDisplay <- "all"), "all" is set by default. You can find the complete list of features and their associated colours in the user guide.
`datasetEnsembl`	Allows the user to manually set which data set is used if required.

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

Tom Hardiman

References

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

Got to ENSEMBLregulation binding motif biomart

Examples

library("Gviz")
gen <- "hg38"
chr <- "chr1"
start <- 10000
end <- 50000
featureDisplay <- "CTCF"

if(interactive()){
 bindMotifsBiomartTrackSingle<-bindingMotifsBiomart_ENSEMBL(gen,chr,start,end,featureDisplay)
  plotTracks(bindMotifsBiomartTrackSingle, from = start, to = end)
} else {
  data(bindMotifsBiomartTrackSingle)
  plotTracks(bindMotifsBiomartTrackSingle, from = start, to = end)
}

######

library("Gviz")
gen <- "hg38"
chr <- "chr1"
start <- 10000
end <- 50000
featureDisplay <- c("CTCF","Egr1")

if(interactive()){
 bindMotifsBiomartTrackMultiple<-bindingMotifsBiomart_ENSEMBL(gen,chr,start,end,featureDisplay)
  plotTracks(bindMotifsBiomartTrackMultiple, from = start, to = end)
} else {
  data(bindMotifsBiomartTrackMultiple)
  plotTracks(bindMotifsBiomartTrackMultiple, from = start, to = end)
}

######

library("Gviz")
gen <- "hg38"
chr <- "chr1"
start <- 10000
end <- 50000
featureDisplay <- "all"

if(interactive()){
 bindMotifsBiomartTrackAll<-bindingMotifsBiomart_ENSEMBL(gen,chr,start,end,featureDisplay)
  plotTracks(bindMotifsBiomartTrackAll, from = start, to = end)
} else {
  data(bindMotifsBiomartTrackAll)
  plotTracks(bindMotifsBiomartTrackAll, 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/bindingMotifsBiomart_ENSEMBL.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bindingMotifsBiomart_ENSEMBL
> ### Title: Creates a binding motif track from ENSEMBL
> ### Aliases: bindingMotifsBiomart_ENSEMBL
> ### Keywords: hplot
> 
> ### ** Examples
> 
> library("Gviz")
> gen <- "hg38"
> chr <- "chr1"
> start <- 10000
> end <- 50000
> featureDisplay <- "CTCF"
> 
> #if(interactive()){
>  bindMotifsBiomartTrackSingle<-bindingMotifsBiomart_ENSEMBL(gen,chr,start,end,featureDisplay)
>   plotTracks(bindMotifsBiomartTrackSingle, from = start, to = end)
> } else {
Error: unexpected '}' in "}"
Execution halted