buildEnrichTable: Creates a 2x2 enrichment contingency table from two gene...

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

Creates a 2x2 enrichment contingency table from two gene lists, or all pairwise contingency tables for a "list" of gene lists.

Description

Creates a 2x2 enrichment contingency table from two gene lists, or all pairwise contingency tables for a "list" of gene lists.

Usage

buildEnrichTable(x, ...)

## Default S3 method:
buildEnrichTable(
  x,
  y,
  listNames = c("gene.list1", "gene.list2"),
  check.table = TRUE,
  geneUniverse,
  orgPackg,
  onto,
  GOLevel,
  showEnrichedIn = TRUE,
  pAdjustMeth = "BH",
  pvalCutoff = 0.01,
  qvalCutoff = 0.05,
  parallel = FALSE,
  nOfCores = 1,
  ...
)

## S3 method for class 'character'
buildEnrichTable(
  x,
  y,
  listNames = c("gene.list1", "gene.list2"),
  geneUniverse,
  orgPackg,
  onto,
  GOLevel,
  showEnrichedIn = TRUE,
  check.table = TRUE,
  pAdjustMeth = "BH",
  pvalCutoff = 0.01,
  qvalCutoff = 0.05,
  parallel = FALSE,
  nOfCores = 1,
  ...
)

## S3 method for class 'list'
buildEnrichTable(
  x,
  check.table = TRUE,
  geneUniverse,
  orgPackg,
  onto,
  GOLevel,
  showEnrichedIn = TRUE,
  pAdjustMeth = "BH",
  pvalCutoff = 0.01,
  qvalCutoff = 0.05,
  parallel = FALSE,
  nOfCores = min(detectCores() - 1, length(x) - 1),
  ...
)

Arguments

x	either an object of class "character" (or coerzable to "character") representing a vector of gene identifiers (e.g., ENTREZ) or an object of class "list". In this second case, each element of the list must be a "character" vector of gene identifiers (e.g., ENTREZ). Then, all pairwise contingency tables between these gene lists are built.
...	Additional parameters for internal use (not used for the moment)
y	an object of class "character" (or coerzable to "character") representing a vector of gene identifiers (e.g., ENTREZ).
listNames	a character(2) with the gene lists names originating the cross-tabulated enrichment frequencies. Only in the "character" or default interface.
check.table	Logical The resulting table must be checked. Defaults to TRUE.
geneUniverse	character vector containing the universe of genes from where gene lists have been extracted. This vector must be obtained from the annotation package declared in orgPackg. For more details see README File.
orgPackg	A string with the name of the genomic annotation package corresponding to a specific species to be analyzed, which must be previously installed and activated. For more details see README File.
onto	string describing the ontology. Either "BP", "MF" or "CC".
GOLevel	An integer, the GO ontology level.
showEnrichedIn	Boolean. If TRUE (default), the cross-table of enriched and non-enriched GO terms vs Gene Lists names (obtained from the enrichedIn function) is automatically saved in the Global Environment.
pAdjustMeth	string describing the adjust method, either "BH", "BY" or "Bonf", defaults to 'BH'.
pvalCutoff	adjusted pvalue cutoff on enrichment tests to report
qvalCutoff	qvalue cutoff on enrichment tests to report as significant. Tests must pass i) pvalueCutoff on unadjusted pvalues, ii) pvalueCutoff on adjusted pvalues and iii) qvalueCutoff on qvalues to be reported
parallel	Logical. Defaults to FALSE but put it at TRUE for parallel computation.
nOfCores	Number of cores for parallel computations. Only in "list" interface.

Details

The arguments 'parallel' and 'nOfCores' are ignored in the 'default' and "character" interfaces, but included for possible future developments; they only apply to the "list" interface. In the "list" interface, 'parallel' defaults to FALSE but there is the possibility of some time saving when the number of gene lists (the length of 'x' in the "list" interface) is high. The trade off between the time spent initializing parallel computing and the possible time gain due to parallelization must be considered in each application and computer.

Value

in the "character" interface, an object of class "table". It represents a 2x2 contingency table, the cross-tabulation of the enriched GO terms in two gene lists: "Number of enriched GO terms in list 1 (TRUE, FALSE)" x "Number of enriched Go terms in list 2 (TRUE, FALSE)". In the "list" interface, the result is an object of class "tableList" with all pairwise tables. Class "tableList" corresponds to objects representing all mutual enrichment contingency tables generated in a pairwise fashion: Given gene lists (i.e. "character" vectors of gene identifiers) l1, l2, ..., lk, an object of class "tableList" is a list of lists of contingency tables t(i,j) generated from each pair of gene lists i and j, with the following structure:

$l2

$l2$l1$t(2,1)

$l3

$l3$l1$t(3,1), $l3$l2$t(3,2)

...

$lk

$lk$l1$t(k,1), $lk$l2$t(k,2), ..., $lk$l(k-1)t(K,k-1)

Methods (by class)

• buildEnrichTable(default): S3 default method

• buildEnrichTable(character): S3 method for class "character"

• buildEnrichTable(list): S3 method for class "list"

Examples

# 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)
?allOncoGeneLists

# Table of joint GO term enrichment between gene lists Vogelstein and sanger,
# for ontology MF at GO level 6.
vog.VS.sang <- buildEnrichTable(allOncoGeneLists[["Vogelstein"]],
                                allOncoGeneLists[["sanger"]],
                                geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
                                onto = "MF", GOLevel = 6, listNames = c("Vogelstein", "sanger"))
vog.VS.sang
# All tables of mutual enrichment:
all.tabs <- buildEnrichTable(allOncoGeneLists,
                             geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
                             onto = "MF", GOLevel = 6)
all.tabs$waldman

pablof1988/goSorensen documentation built on July 31, 2024, 10:26 p.m.