coMET (version 1.4.4)

chromHMM_RoadMap: 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')

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.

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 <- 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 <- "chr1"
start <- 4500000
end <- 4600000
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 <- "chr1"
start <- 4500000
end <- 4600000
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)
}