Create contactsRegulome Object

This function uses virtual 4C data (3 bigWig files, scores 0, 3 and 5) to generate an object containing the data present in coordinates and all the elements needed for its plotting method.

create_contactsRegulome(coordinates, contacts_dataset,
  contacts_col = c(`0` = "grey", `3` = "blue", `5` = "dark orange"),
  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.
contacts_dataset

BaitID or bait gene name for the virtual 4C data (Miguel-Escalada et al. (2019)) to plot.
contacts_col

Named vector ("0", "3" and "5"), with the colors for each group of CHiCAGO contacts.
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 contactsRegulome, which is basically a list with the following attributes:

  • name: Name of bait for the selected virtual4C data.

  • col: Color for plotting virtual4C data, grouping by chicago scores (0=0-3; 3=3-5; 5=>5).

  • genome: Genome build.

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

  • value: GRanges object containing all CHiCAGO scores in coordinates.

  • moreArgs: Additional arguments, which are:

    • viewpoint: Position for the bait, will drow a triangle in this position.

    • maxContact: Maximum CHiCAGO score in coordinates that will be used for scaling SNP data in case it is also plot.

Examples

if (FALSE) {
cont <- create_contactsRegulome(coordinates="chr20:22461643-22666093",
                                contacts_dataset="FOXA2",
                                path="~/data/IRB_database/")
}