chromHMM_RoadMap {coMET} | R Documentation

## Creates a ChromHMM track from a file of RoadMap

### Description

Creates a ChromHMM 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

    chromHMM_RoadMap(gen="hg19",chr, start, end, bedFilePath,
    featureDisplay = 'all', colorcase='roadmap15',
    title=" chromHMM 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.
`colorcase` | the type of colors used to visualise different elements contained in ROADmap data with 15-,18-,25- states. choice between roadmap15, roadmap18, comet18, roadmap25 and comet25.
`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 <- 4500000
    end <- 4600000
    featureDisplay <- "7_Enh"

    extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
    bedFilePath <- file.path(extdata, "RoadMap/E063_15_coreMarks_mnemonics.bed")

    if(interactive()){
      chromHMM_RoadMapSingle <- chromHMM_RoadMap(gen="hg19",chr,start, end,
      bedFilePath, featureDisplay = featureDisplay, colorcase='roadmap15' )
      plotTracks(chromHMM_RoadMapSingle, from = start, to = end)
    } else {
      data(chromHMM_RoadMapSingle)
      plotTracks(chromHMM_RoadMapSingle, from = start, to = end)
    }

    ######

    library("Gviz")
    chr <- "chr22"
    start <- 38291000
    end <- 38301200
    featureDisplay <- c("7_Enh","13_ReprPC")

    extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
    bedFilePath <- file.path(extdata, "RoadMap/E063_15_coreMarks_mnemonics.bed")

    if(interactive()){
      chromHMM_RoadMapMultiple <- chromHMM_RoadMap(gen="hg19",chr,start, end,
      bedFilePath, featureDisplay = featureDisplay, colorcase='roadmap15' )
      plotTracks(chromHMM_RoadMapMultiple, from = start, to = end)
    } else {
      data(chromHMM_RoadMapMultiple)
      plotTracks(chromHMM_RoadMapMultiple, from = start, to = end)
    }

    #####

    library("Gviz")
    chr <- "chr22"
    start <- 38291000
    end <- 38301200
    featureDisplay <- "all"

    extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
    bedFilePath <- file.path(extdata, "RoadMap/E063_15_coreMarks_mnemonics.bed")

    if(interactive()){
      chromHMM_RoadMapAll <- chromHMM_RoadMap(gen="hg19",chr,start, end,
      bedFilePath, featureDisplay = featureDisplay, colorcase='roadmap15' )
      plotTracks(chromHMM_RoadMapAll, from = start, to = end)
    } else {
      data(chromHMM_RoadMapAll)
      plotTracks(chromHMM_RoadMapAll, from = start, to = end)
    }

[Package coMET version 1.12.0 Index]