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

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",
  genome.build = "character",
  organism = "character"
),
  package = "chipenrich.data"
);

Genesets

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

The GeneSet class has the following definition:

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

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).

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, $b$.

Example data for chipenrich

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



wangk4/chipenrich.data documentation built on June 19, 2020, 12:18 a.m.