getTable: Access to the contingency table of mutual enrichment of one...

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

Access to the contingency table of mutual enrichment of one or more equivalence test results

Description

Given objects representing the result(s) of one or more equivalence tests (classes "equivSDhtest", "equivSDhtestList" or "allEquivSDtest", i.e., the result of functions 'equivTestSorensen' and 'allEquivTestSorensen') this function returns the contingency tables from which the tests were performed.

Usage

getTable(x, ...)

## S3 method for class 'equivSDhtest'
getTable(x, ...)

## S3 method for class 'equivSDhtestList'
getTable(x, ...)

## S3 method for class 'AllEquivSDhtest'
getTable(x, onto, GOLevel, listNames, ...)

Arguments

x	an object of class "equivSDhtest" or "equivSDhtestList" or "allEquivSDtest".
...	Additional parameters.
onto	character, a vector with one or more of "BP", "CC" or "MF", ontologies to access.
GOLevel	numeric or character, a vector with one or more GO levels to access. See the details section and the examples.
listNames	character(2), the names of a pair of gene lists.

Details

Argument GOLevel can be of class "character" or "numeric". In the first case, the GO levels must be specified like "level 6" or c("level 4", "level 5", "level 6") In the second case ("numeric"), the GO levels must be specified like6 or 4:6.

Value

An object of class "table", the 2x2 enrichment contingeny table of mutual enrichment in two gene lists, built to perform the equivalence test based on the Sorensen-Dice dissimilarity.

When x is an object of class "equivSDhtest" (i.e., the result of a single equivalence test), the returned value is an object of class "table", the 2x2 enrichment contingeny table of mutual enrichment in two gene lists, built to perform the equivalence test based on the Sorensen-Dice dissimilarity. For an object of class "equivSDhtestList" (i.e. all pairwise tests for a set of gene lists), the resulting value is a list with all the tables built in all those tests. If x is an object of class "allEquivSDtest" (i.e., the test iterated along GO ontologies and levels), the preceding result is returned as a list along the ontologies, levels and pairs of gene lists specified by the arguments onto, GOlevel and listNames (or all ontologies, levels or pairs of gene lists present in x if one or more of these arguments are missing).

Methods (by class)

• getTable(equivSDhtest): S3 method for class "equivSDhtest"

• getTable(equivSDhtestList): S3 method for class "equivSDhtestList"

• getTable(AllEquivSDhtest): S3 method for class "AllEquivSDhtest"

Examples

# Dataset 'allOncoGeneLists' contains the result of the equivalence test between gene lists
# 'waldman' and 'atlas', at level 4 of the BP ontology:
data(waldman_atlas.BP.4)
waldman_atlas.BP.4
class(waldman_atlas.BP.4)
# This may correspond to the result of code like:
# waldman_atlas.BP.4 <- equivTestSorensen(
#   allOncoGeneLists[["waldman"]], allOncoGeneLists[["atlas"]],
#   geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
#   onto = "BP", GOLevel = 4, listNames = c("waldman", "atlas"))
# (But results may vary according to GO updating)
getTable(waldman_atlas.BP.4)

# All pairwise equivalence tests at level 4 of the BP ontology
data(BP.4)
?BP.4
class(BP.4)
# This may correspond to a call like:
# BP.4 <- equivTestSorensen(allOncoGeneLists,
#                           geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
#                           onto = "BP", GOLevel = 4)
getTable(BP.4)

# Equivalence test iterated over all GO ontologies and levels 3 to 10:
data(cancerEquivSorensen)
?cancerEquivSorensen
class(cancerEquivSorensen)
# This may correspond to code like:
# cancerEquivSorensen <- allEquivTestSorensen(allOncoGeneLists,
#                                             geneUniverse = humanEntrezIDs,
#                                             orgPackg = "org.Hs.eg.db")
# (By default, the tests are iterated over all GO ontologies and for levels 3 to 10)
# All 2x2 contingecy tables of joint enrichment:
getTable(cancerEquivSorensen)
# Contingency tables only for some GO ontologies, levels or pairs of gene lists:
getTable(cancerEquivSorensen, GOLevel = "level 6")
getTable(cancerEquivSorensen, GOLevel = 6)
getTable(cancerEquivSorensen, GOLevel = seq.int(4,6), listNames = c("waldman", "sanger"))
getTable(cancerEquivSorensen, GOLevel = "level 6", onto = "BP")
getTable(cancerEquivSorensen, GOLevel = "level 6", onto = "BP",
         listNames = c("waldman", "sanger"))

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