Create mapsRegulome Object

This function loads chromatin maps, obtains the classes present in coordinates and adds the needed parameters for plotting.

create_mapsRegulome(coordinates, maps_dataset, genome = "hg19",
  path = "~/data/IRB/")

Arguments

coordinates	Either a GRanges object, data.frame or character string (i.e. chr11:17227951-17589050) indicating the coordinates for the region the user wants to plot.
maps_dataset	Name of the chromatin maps to plot. The value should be one of the defined below (column Dataset). Defaults to "", which will produce an empty plot. Name Dataset Reference Adult Islets - Chromatin Classes chromatinClassesReduced Miguel-Escalada et al. (2019) Adult Islets - Chromatin Classes openChromatinClasses Pasquali et al. (2014) Pancreatic Progenitors progenitors Cebola et al. (2015) Adult Islets - Chromatin States chromatinStates Parker et al. (2013)
genome	Character string indicating the genome for the coordinates. Default: hg19.
path	Path containing the genomes folder (for example "hg19"). Default: "~/data/IRB/"

Value

An object of class mapsRegulome, which is basically a list with the following attributes:

• name: Name of selected chromatin map dataset.

• col: Named vector with the color of each type of chromatin class.

• genome: Genome build.

• coordinates: Selected coordinates to plot as a GRanges object.

• value: GRanges object containing coordinates and type of chromatin class.

• moreArgs: Additional arguments, which are empty.

Examples

if (FALSE) {
maps <- create_mapsRegulome(coordinates="chr20:22461643-22666093",
                            maps_dataset="openChromatinClasses",
                            path="~/data/IRB_database/")
}