allBuildEnrichTable: Iterate 'buildEnrichTable' along the specified GO ontologies...

In pablof1988/goSorensen: Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

Iterate buildEnrichTable along the specified GO ontologies and GO levels

Description

Iterate buildEnrichTable along the specified GO ontologies and GO levels

Usage

allBuildEnrichTable(
  x,
  check.table = TRUE,
  ontos = c("BP", "CC", "MF"),
  GOLevels = seq.int(3, 10),
  trace = TRUE,
  ...
)

Arguments

x	object of class "list". Each of its elements must be a "character" vector of gene identifiers. Then all pairwise contingency tables of joint enrichment are built between these gene lists, iterating the process for all specified GO ontologies and GO levels.
check.table	Boolean. If TRUE (default), all resulting tables are checked by means of function nice2x2Table.
ontos	"character", GO ontologies to analyse. Defaults to c("BP", "CC", "MF").
GOLevels	"integer", GO levels to analyse inside each of these GO ontologies.
trace	Logical. If TRUE (default), the (usually very time consuming) process of function allBuildEnrichTable is traced along the specified GO ontologies and levels.
...	extra parameters for function buildEnrichTable.

Value

An object of class "allTableList". It is a list with as many components as GO ontologies have been analysed. Each of these elements is itself a list with as many components as GO levels have been analised. Finally, the elements of these lists are objects as generated by buildEnrichTable.list, i.e., objects of class "tableList" containing all pairwise contingency tables of mutual enrichmen between the gene lists in argument x.

Examples

# This example is extremely time consuming, it scans two GO ontologies and three
# GO levels inside them to obtain the contingency tables of mutual enrichment.
# Gene universe:
# data(humanEntrezIDs)
# Gene lists to be explored for enrichment:
# data(pbtGeneLists)
# allBuildEnrichTable(pbtGeneLists,
#                     geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
#                     ontos = c("MF", "BP"), GOLevels = seq.int(4,6))

pablof1988/goSorensen documentation built on July 21, 2023, 8:38 a.m.