Create snpsRegulome Object

This function loads the GWAS information for SNPs from the specified dataset, selects those present in coordinates and adds all the elements needed for plotting.

create_snpsRegulome(coordinates, snps_dataset = "",
  snps_col = "dark red", genome = "hg19", top = 3,
  snps_scaling = NULL, 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.
snps_dataset	GWAS SNPs dataset name to use for the analysis. The value should be one of the defined below (column Dataset). Defaults to "", which will produce an empty plot. Name Dataset Reference 70KforT2D 70KforT2D S. Bonàs-Guarch et al. (2018) Diagram diagram A. P. Morris et al. (2012) Magic magic R. A. Scott et al. (2012)
snps_col	Color for the GWAS SNPs. Default: "dark red"
genome	Character string indicating the genome for the coordinates. Default: hg19.
top	Number indicating how many of the most significant SNPs in the region will be shown as labels.
snps_scaling	Number indicating the value to which scale the maximum -log10 PVAL for SNPs. Defaults to NULL, meaning that no scaling will be performed.
path	Path containing the genomes folder (for example "hg19"). Default: "~/data/IRB/"

Value

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

• name: Name of the selected SNP dataset.

• col: Color for plotting the SNPs.

• genome: Genome build.

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

• value: GRanges object containing all SNP values in coordinates.

• moreArgs: Additional arguments, which are:

  • top: contains the number of SNPs with lower P-values whose name will be plot

  • scaleTo: parameter that includes a scaling parameter in case virtual4C is also plot along SNPs (it is the maximum virtual4C value and if no virtual4C is plot, is the maximum SNP -log10 p-value).

Examples

if (FALSE) {
snps <- create_snpsRegulome(coordinates="chr20:22461643-22666093",
                            snps_dataset="diagram",
                            path="~/data/IRB_database/")
}