coMET (version 1.4.4)

ChIPTF_ENCODE: 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

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)
}