coMET (version 1.4.4)

DNaseI_RoadMap: Creates a promoter/enhancer regions track from a file of RoadMap

Description

Creates a track of promoter/enhancer regions 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

DNaseI_RoadMap(gen="hg19", chr, start, end, bedFilePath, featureDisplay='promotor',showId=TRUE, 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

featureDisplay

A vector of features to be displayed, such as 1_TssA. Spelling and capitalisation of features must be identical to those in the user guide (in the 'State & Acronym' column). There are three possibilities. First, the visualisation of only one feature (e.g. featureDisplay <- "1_TssA"), 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("1_TssA","2_TssAFlnk")). 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.

showId

Allows to visualise the Id of DNAse 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 <- 707612
end <- 722151
gen="hg19"

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "RoadMap/regions_prom_E063.bed")

if(interactive()){
  DNaseI_RoadMapSingle <- DNaseI_RoadMap(gen,chr,start, end, bedFilePath, featureDisplay='promotor'  )
  plotTracks(DNaseI_RoadMapSingle, from = start, to = end)
} else {
  data(DNaseI_RoadMapSingle)
  plotTracks(DNaseI_RoadMapSingle, from = start, to = end)
}