In afukushima/MSEApdata: Metabolite-set data collection for pathway analysis in metabolomics

The MSEApdata package is the companion to MSEAp. It contains the following, which are necessary for metabolite-set enrichment analysis with MSEAp:

Metabolite-set data

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"
);

• nearest_tss: The locus is the region spanning the midpoints between the TSSs of adjacent genes.
• nearest_gene: The locus is the region spanning the midpoints between the boundaries of each gene, where a gene is defined as the region between the furthest upstream TSS and furthest downstream TES for that gene. If two gene loci overlap each other, we take the midpoint of the overlap as the boundary between the two loci. When a gene locus is completely nested within another, we create a disjoint set of 3 intervals, where the outermost gene is separated into 2 intervals broken apart at the endpoints of the nested gene.

Genesets

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

The GeneSet class has the following definition:

Example data for chipenrich

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

afukushima/MSEApdata documentation built on May 3, 2019, 11:52 p.m.