chromHMM_RoadMap: Creates a ChromHMM track from a file of RoadMap

In TiphaineCMartin/coMET_original: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

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

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 <- "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)
}

TiphaineCMartin/coMET_original documentation built on May 9, 2019, 4:49 p.m.