Create clustersRegulome Object

This function loads the selected cluster classification, selects the clusters present in coordinates and adds the needed parameters for plotting.

create_clustersRegulome(coordinates, clusters_dataset,
  cluster_col = "dark green", 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.
clusters_dataset	Name of the enhncer cluster data to plot. The value should be one of the defined below (column Dataset). Defaults to "", which will produce an empty plot. Name Dataset Reference Enhancer Hubs enhancerHubs Miguel-Escalada et al. (2019) Super Enhancers superEnhancers Miguel-Escalada et al. (2019) Enhancer Clusters enhancerClusters Pasquali et al. (2014) Stretch Enhancers stretchEnhancers Parker et al. (2013) COREs cores K. J. Gaulton et al. (2010)
cluster_col	Color for the clusters. Default: "dark green"
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 clustersRegulome, which is basically a list with the following attributes:

• name: Name of selected enhancer cluster dataset.

• col: Character vector with the color of the enhancer clusters.

• genome: Genome build.

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

• value: GRanges object containing coordinates for the enhancer clusters and the class of the line that will be drawn.

• moreArgs: Additional arguments, which include:

  • lwd: Information on the linewidth for each class of enhancer cluster feature.

Examples

if (FALSE) {
clust <- create_clustersRegulome(coordinates="chr20:22461643-22666093",
                                 clusters_dataset="enhancerHubs",
                                 path="~/data/IRB_database/")
}