DNaseI_RoadMap {coMET} | R Documentation

## 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",
    title = "DNaseI RoadMap")

### 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
`title` | The name of the annotation track

### Value

An AnnotationTrack object of Gviz

### Author(s)

Tiphaine Martin

Tom Hardiman

### References

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

Got to RoadMap Epigenome

### Examples

    library("Gviz")
    chr <- "chr2"
    start <- 38300049
    end <- 38302592
    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)
    }

[Package coMET version 1.16.0 Index]