ChIPTF_ENCODE: Creates a TF motif track from ENCODE

In coMET: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

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", title="TF motifs ENCODE")

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"))
title	The name of the annotation track

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)
}

coMET documentation built on Nov. 8, 2020, 5 p.m.