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Last data update: 2014.03.03

R: Creates a TF motif track from ENCODE

ChIPTF_ENCODE

R Documentation

Creates a TF motif track from ENCODE

Description

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

Usage

ChIPTF_ENCODE(gen="hg19", chr, start, end, bedFilePath, featureDisplay='all', motifColorFile, type_stacking='dense',showId=FALSE,just_group="above")

Arguments

`gen`	the name of the genome. Default value=hg19
`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)
`bedFilePath`	The path of the BED file from Kheradpour and Kellis, 2014.
`featureDisplay`	A vector of regulatory features to be displayed, such as Predicted heterochomatin. 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 <- "Predicted heterochomatin"), 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("Predicted low activity","Predicted heterochomatin")). 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.
`motifColorFile`	The path of the BED file with 2 columns ( the first for motif name and the second for the color in hex format without # in the beginning) with a header.
`type_stacking`	Object of class"character", the stacking type of overlapping items on the final plot.One in c(hide, dense, squish, pack,full). More information cf the option "stacking" in Gviz
`showId`	logical. say if we write the name of group
`just_group`	position. say where we write the name of group (choice in c("above","righ","left"))

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

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

Got to BindingMotifsBiomart binding motif biomart

Examples

library("Gviz")
gen <- "hg19"
chr<-"chr1"
start <- 1000
end <- 329000


if(interactive()){
    extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
    bedFilePath <- file.path(extdata, "ENCODE/motifs1000_matches_ENCODE.txt")
    motif_color <- file.path(extdata, "ENCODE/TFmotifs_colors.csv")
    chipTFtrack <- ChIPTF_ENCODE(gen,chr,start, end, bedFilePath, featureDisplay=c("AHR::ARNT::HIF1A_1","AIRE_1","AIRE_2","AHR::ARNT_1"), motif_color,type_stacking="squish",showId=TRUE)
    plotTracks(chipTFtrack, from = start, to = end)
} else {
    data(chipTFtrack)
    plotTracks(chipTFtrack, 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/ChIPTF_ENCODE.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ChIPTF_ENCODE
> ### Title: Creates a TF motif track from ENCODE
> ### Aliases: ChIPTF_ENCODE
> ### Keywords: hplot
> 
> ### ** Examples
> 
> library("Gviz")
> gen <- "hg19"
> chr<-"chr1"
> start <- 1000
> end <- 329000
> 
> 
> #if(interactive()){
>     extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
>     bedFilePath <- file.path(extdata, "ENCODE/motifs1000_matches_ENCODE.txt")
>     motif_color <- file.path(extdata, "ENCODE/TFmotifs_colors.csv")
>     chipTFtrack <- ChIPTF_ENCODE(gen,chr,start, end, bedFilePath, featureDisplay=c("AHR::ARNT::HIF1A_1","AIRE_1","AIRE_2","AHR::ARNT_1"), motif_color,type_stacking="squish",showId=TRUE)
Error in file(file, "rt") : cannot open the connection
Calls: ChIPTF_ENCODE -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/home/ddbj/local/lib64/R/library/coMET/extdata/ENCODE/motifs1000_matches_ENCODE.txt': No such file or directory
Execution halted