Description Usage Arguments Value Author(s) References Examples
View source: R/BiofeatureGraphics.R
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.
1 2 3 | DNaseI_RoadMap(gen="hg19", chr, start, end, bedFilePath,
featureDisplay='promotor',showId=TRUE, type_stacking="dense",
title = "DNaseI RoadMap")
|
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 |
An AnnotationTrack object of Gviz
Tiphaine Martin
Tom Hardiman
http://bioconductor.org/packages/release/bioc/html/Gviz.html
Got to RoadMap Epigenome
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | 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)
}
|
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