dgfootprints_RoadMap {coMET} | R Documentation

## 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",
    title= "DGFP 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
`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
`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 <- "chr1"
    start <- 236728
    end <- 238778
    gen="hg19"

    extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
    bedFilePath <- file.path(extdata, "RoadMap/CD3-DS17198.hg19_subset.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)
    }

[Package coMET version 1.16.0 Index]