create_contactsRegulome: Create contactsRegulome Object

In mireia-bioinfo/plotRegulome: Plot Islet Regulome data

Create contactsRegulome Object

Description

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.

Usage

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

## Not run: 
cont <- create_contactsRegulome(coordinates="chr20:22461643-22666093",
                                contacts_dataset="FOXA2",
                                path="~/data/IRB_database/")

## End(Not run)

mireia-bioinfo/plotRegulome documentation built on July 3, 2024, 3:34 p.m.