dgfootprints_RoadMap: Creates a track of DNA motif positional bias in digital...

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

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,
    fontfamily="sans",fontfamily.title="sans")
} else {
  data(dgfootprints_RoadMapSingle)
  plotTracks(dgfootprints_RoadMapSingle, from = start, to = end,
    fontfamily="sans",fontfamily.title="sans")
}

TiphaineCMartin/coMET documentation built on April 27, 2022, 6:45 a.m.