The package is the companion to chipenrich. It contains the following, which are necessary for gene set enrichment with chipenrich:

1 Locus definitions

chipenrich::supported_locusdefs() lists all available locus definitions for chipenrich::supported_genomes().

The LocusDefinition class has the following definition:

methods::setClass("LocusDefinition", methods::representation(
  dframe = "data.frame",
  granges = "GRanges", = "character",
  organism = "character"
  package = ""

2 Genesets

chipenrich::supported_genesets() lists all available genesets for chipenrich::supported_genomes().

The GeneSet class has the following definition:

# S4 class for storing genesets.
  set.gene = "environment",
  type = "character", = "environment",
  all.genes = "character",
  organism = "character",
  dburl = "character"
), methods::prototype(
  set.gene = new.env(parent=emptyenv()),
  type = "", = new.env(parent=emptyenv()),
  all.genes = "",
  organism = "",
  dburl = ""
  package = ""

3 TSS data

The TSS objects are used to create QC plots in chipenrich() giving the distribution of peak distances to TSSs. TSS objects are GRanges with mcols for gene_id (Entrez Gene ID) and symbol (gene symbols).

4 Mappability data

chipenrich::supported_supported_read_lengths() lists the available mappability data. The mappability data is a data.frame with columns geneid and mappa. We define base pair mappability as the average read mappability of all possible reads of size K that encompass a specific base pair location, \(b\).

5 Example data for chipenrich

We include two example peak sets, peaks_E2F4 and peaks_H3K4me3_GM12878, both for genome hg19.