coMET (version 1.4.4)

dgfootprints_RoadMap: Creates a track of DNA motif positional bias in digital genomic Footprinting Sites (DGFP) from a file of RoadMap

Description

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

Usage

dgfootprints_RoadMap(gen="hg19", chr, start, end, bedFilePath, tissueGroupDisplay='Blood & T-cell',showId=FALSE, type_stacking="dense")

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 file path to the .BED file containing the data to be visualised

tissueGroupDisplay

the group of tissue visualised among list("Neurosph","Epithelial","IMR90","Thymus","Heart","Brain","Digestive","Muscle","Other","iPSC","HSC & B-cell","Blood & T-cell"="ES-deriv")

showId

logical. say if we write the name of group

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

Value

An AnnotationTrack object of Gviz

References

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

Got to RoadMap Epigenome

Examples

library("Gviz")
chr <- "chr1"
start <- 236728
end <- 238778
gen="hg19"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "RoadMap/CD3-DS17198.hg19.bed")

if(interactive()){
  dgfootprints_RoadMapSingle <- dgfootprints_RoadMap(gen,chr,start, end, bedFilePath, tissueGroupDisplay='Blood & T-cell' )
  plotTracks(dgfootprints_RoadMapSingle, from = start, to = end)
} else {
  data(dgfootprints_RoadMapSingle)
  plotTracks(dgfootprints_RoadMapSingle, from = start, to = end)
}