GOMembershipMatrix: Construct a new gene set membership matrix
In dgrtwo/GSEAMA: Gene set enrichment analysis made awesome

Description Usage Arguments Examples

Construct a gene set membership matrix (one row per gene, one column per gene set, with 1 indicating membership) from a GO annotation map.

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GOMembershipMatrix(annotations, ontology = c("BP", "MF", "CC"),
  evidence = NULL, min_size = 1, max_size = Inf, ancestors = TRUE,
  chosen_genes = NULL)

`annotations`	A Go3AnnDbBimap object, typically from a Bioconductor Annotation package. For example, org.Hs.egGO from org.Hs.eg.db for human genes.
`ontology`	A vector of ontologies to include; should be a subset of c("BP", "MF", "CC")
`evidence`	A vector of GO evidence codes to include
`min_size`	Minimum size of a gene set to be included
`max_size`	Maximum size of a gene set to be included
`ancestors`	Whether a gene included in a gene set should also be included as being in all ancestors of that gene set (default TRUE)
`chosen_genes`	If provided, restricts genes to those in chosen_genes The GO annotation maps typically come from the Bioconductor AnnotationDB packages. A couple of notable examples are: Homo sapiens: org.Hs.egGO S. cerevisiae: org.Sc.sgdGO E coli K12: org.EcK12.egGO You can restrict the sets to the BP (Biological Process), MF (Molecular Function), or CC (Cellular Compartment) ontologies (by default all are included).

# yeast membership matrix
library(org.Sc.sgd.db)
mm <- GOMembershipMatrix(org.Sc.sgdGO, min_size = 5, max_size = 250)

# restrict to Biological Process ontology:
mm <- GOMembershipMatrix(org.Sc.sgdGO, ontology = "BP", min_size = 5, max_size = 250)

# human membership matrix
library(org.Hs.eg.db)
mm <- GOMembershipMatrix(org.Hs.sgdGO, min_size = 5, max_size = 250)