Create genesRegulome Object

This funciton loads all genes in chr, selects those transcripts present in coordinates and adds the needed parameters for plotting.

create_genesRegulome(coordinates, genes_col = c(gene = "dark grey", spec
  = "darkorchid3", lnc = "black"), showLongestTranscript = TRUE,
  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.
genes_col

Named character vector ("gene", "lnc" and "spec") with the colors for each type of feture plotted in the gene annotation track.
showLongestTranscript

When plotting gene data, set to TRUE (default) if you want to reduce the number of transcripts by only plotting the longest transcript per gene. If set to FALSE, will plot all available transcripts.
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 mapsRegulome, which is basically a list with the following attributes:

  • name: Gene Annotation.

  • col: Named vector with the color of each group of gene annotation, currently "gene", "spec", and "lnc".

  • genome: Genome build.

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

  • value: GRanges object containing coordinates for the gene annotations, together with the type of gene annotation (EXON or GENE) and the group..

  • moreArgs: Additional arguments, which are empty.

Examples

if (FALSE) {
    genes <- create_genesRegulome(coordinates="chr20:22461643-22666093",
                                  path="~/data/IRB_database/")
}