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),
  storeEnrichedIn = TRUE,
  trace = TRUE,
  ...
)

Arguments

x	object of class "list". Each of its elements must be a "character" vector of gene identifiers (e.g., ENTREZ). 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.
storeEnrichedIn	logical, for each ontology and level under study, the matrix of enriched (GO terms) x (gene lists) TRUE/FALSE values, must be stored in the result?
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 enrichment between the gene lists in argument x.

Examples

# This example is highly time-consuming. It scans two GO ontologies and three
# GO levels inside them to obtain the contingency tables of joint enrichment.

# Obtaining ENTREZ identifiers for the gene universe of humans:
# library(org.Hs.eg.db)
# humanEntrezIDs <- keys(org.Hs.eg.db, keytype = "ENTREZID")

# Gene lists to be explored for enrichment:
# data(allOncoGeneLists)

# Computing Contingency Tables for all the possible pairwise comparisons for
# the ontologies MF, BP, and the GO levels from 4 to 6:
# someOntosAndLevels <- allBuildEnrichTable(allOncoGeneLists,
#                                           geneUniverse = humanEntrezIDs, 
#                                           orgPackg = "org.Hs.eg.db",
#                                           ontos = c("MF", "BP"), 
#                                           GOLevels = seq.int(4,6))
# someOntosAndLevels$BP$`level 4`
# attr(someOntosAndLevels$BP$`level 4`, "enriched")
#
# To avoid storage-consuming redundancies, the table of GO terms x gene lists 
# enrichment is not stored for the full set of gene list pairs at each 
# ontology and level
# someOntosAndLevels$BP$`level 4`$Vogelstein
# attr(someOntosAndLevels$BP$`level 4`$Vogelstein, "enriched")
# someOntosAndLevels$BP$`level 4`$Vogelstein$atlas
# attr(someOntosAndLevels$BP$`level 4`$Vogelstein$atlas, "enriched")
#
# When the "ontos" and/or "GOLevels" arguments are not supplied, the function 
# computes by default every possible contingency table between the lists 
# being compared for the three ontologies (BP, CC, MF) and/or GO levels from
# 3 to 10.

pablof1988/goSorensen documentation built on Dec. 15, 2024, 12:01 p.m.