enrichedIn: This function builds a cross-tabulation of enriched (TRUE)...

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

This function builds a cross-tabulation of enriched (TRUE) and non-enriched (FALSE) GO terms vs. gene lists

Description

This function builds a cross-tabulation of enriched (TRUE) and non-enriched (FALSE) GO terms vs. gene lists

Usage

enrichedIn(x, ...)

## Default S3 method:
enrichedIn(
  x,
  geneUniverse,
  orgPackg,
  onto,
  GOLevel,
  pAdjustMeth = "BH",
  pvalCutoff = 0.01,
  qvalCutoff = 0.05,
  parallel = FALSE,
  nOfCores = 1,
  onlyEnriched = TRUE,
  ...
)

## S3 method for class 'character'
enrichedIn(
  x,
  geneUniverse,
  orgPackg,
  onto,
  GOLevel,
  pAdjustMeth = "BH",
  pvalCutoff = 0.01,
  qvalCutoff = 0.05,
  parallel = FALSE,
  nOfCores = 1,
  onlyEnriched = TRUE,
  ...
)

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

Arguments

x	either an object of class "character" (or coerzable to "character") or "list". In the "character" interface, these values should represent Entrez gene (or, in general, feature) identifiers. In the "list" interface, each element of the list must be a "character" vector of Entrez identifiers
...	Additional parameters
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, refer to vignette goSorensen_Introduction.
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, refer to vignette goSorensen_Introduction.
onto	string describing the ontology. Belongs to c('BP', 'MF', 'CC')
GOLevel	GO level, an integer
pAdjustMeth	string describing the adjust method. Belongs to c('BH', 'BY', 'Bonf')
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. Only in "list" interface. Defaults to FALSE, put it at TRUE for parallel computation
nOfCores	Number of cores for parallel computations. Only in "list" interface
onlyEnriched	logical. If TRUE (the default), the returned result only contains those GO terms enriched in almost one of the gene lists

Details

When the function argument onlyEnriched is FALSE, commonly the result is a sparse but very large object. This function is primarily designed for internal use of function buildEnrichTable, with argument onlyEnriched always put at its default TRUE value. Then calls to enrichedIn result in much more compact objects, in general.

Argument parallel only applies to interface "list". Its default value ís "FALSE" and you may consider the trade of between the time spent in initializing parallelization and the possible time gain when parallelizing. It is difficult to establish a general guideline, but parallelizing is only worthwhile when analyzing many gene lists, on the order of 30 or more, although it depends a lot on each processor.

Value

In the "character" interface, a length k vector of TRUE/FALSE values corresponding to enrichment or not of the GO terms at level 'GOLev' in ontology 'onto'. If 'onlyEnriched' is FALSE, k corresponds to the total number of these GO terms. If 'onlyEnriched' is TRUE (default) k is the number of enriched GO terms (and then all values in the resulting vector are TRUE). In the "list" interface, a logical matrix of TRUE/FALSE values indicating enrichment or not, with k rows and s columns. s is the number of gene lists (the length of "list" 'x'). If 'onlyEnriched' is FALSE, k corresponds to the total number of GO terms at level 'GOLev' in ontology 'onto'. If 'onlyEnriched' is TRUE (default), the resulting matrix only contains the k rows corresponding to GO terms enriched in almost one of these s gene lists. In both interfaces ("character" or "list"), the result also has an attribute (nTerms) with the total number of GO terms at level 'GOLev' in ontology 'onto'.

Methods (by class)

• enrichedIn(default): S3 default method

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

• enrichedIn(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

# Computing the cross table:
enrichd <- enrichedIn(allOncoGeneLists[["Vogelstein"]],
                      geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
                      onto = "MF", GOLevel = 6)
enrichd

# Cross table of enriched GO terms (GO ontology MF, level 6) for all gene
# lists in 'allOncoGeneLists':
enrichedAllOncoMF.6 <- enrichedIn(allOncoGeneLists,
                          geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
                          onto = "MF", GOLevel = 6)
enrichedAllOncoMF.6
object.size(enrichedAllOncoMF.6)
# How many GO terms were tested for enrichment at ontology MF and level 6:
attr(enrichedAllOncoMF.6, "nTerms")

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