Create tfsRegulome Object

This function load the TFBS data, selects those binding sites present in coordinates and adds the needed parameters for plotting.

create_tfsRegulome(coordinates, tfs_dataset, tfs_col = "dark blue",
  position_y = 0.5, 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.
tfs_dataset	Name of the TF dataset 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 – Structural structure Miguel-Escalada et al. (2019) Pancreatic Progenitors progenitors Cebola et al. (2015) Adult Islets – Tissue-specific adult Pasquali et al. (2014)
tfs_col	Color for the TFs circle border.
position_y	Number from 0 (bottom) to 1 (top) indicating the position at which the circles should be plotted. Default = 0.5.
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 tfsRegulome, which is basically a list with the following attributes:

• name: Name of selected transcription factor 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 transcription factor binding sites and the name of the TF that is binding.

• moreArgs: Additional arguments, which include:

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

Examples

if (FALSE) {
    tfs <- create_tfsRegulome(coordinates="chr20:22461643-22666093",
                              tfs_dataset="adult",
                              path="~/data/IRB_database/")
}