getEffNboot: Access to the number of effective bootstrap replicates in one...

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

Access to the number of effective bootstrap replicates in one or more equivalence test results (only for their bootstrap version)

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 number of effective bootstrap replicates. Obviously, this only applies to calls of these functions with the parameter boot = TRUE, otherwise it returns a NA value. See the details section for further explanation.

Usage

getEffNboot(x, ...)

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

## S3 method for class 'equivSDhtestList'
getEffNboot(x, simplify = TRUE, ...)

## S3 method for class 'AllEquivSDhtest'
getEffNboot(x, onto, GOLevel, listNames, simplify = TRUE, ...)

Arguments

x	an object of class "equivSDhtest" or "equivSDhtestList" or "allEquivSDtest".
...	Additional parameters.
simplify	logical, if TRUE the result is simplified, e.g., returning a vector instead of a matrix.
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

In the bootstrap version of the equivalence test, resampling is performed generating new bootstrap contingency tables from a multinomial distribution based on the "real", observed, frequencies of mutual enrichment. In some bootstrap resamples, the generated contingency table of mutual enrichment may have very low frequencies of enrichment, which makes it unable for Sorensen-Dice computations. Then, the number of effective bootstrap resamples may be lower than those initially planned. To get the number of initially planned bootstrap resamples use function getNboot.

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 seq.int(4,6).

Value

When x is an object of class "equivSDhtest" (i.e., the result of a single equivalence test), the returned value is a single numeric value, the number of effective bootstrap replicates, or NA if bootstrapping has not been performed. For an object of class "equivSDhtestList" (i.e. all pairwise tests for a set of gene lists), if simplify = TRUE (the default), the resulting value is a vector with the number of effective bootstrap replicates in all those tests, or the symmetric matrix of all these values if simplify = TRUE. If x is an object of class "allEquivSDtest" (i.e., the test iterated along GO ontologies and levels), the preceding result is returned in the form of a list along the ontologies, levels and pairs of gene lists specified by the arguments onto, GOlevel and listNames (or all present in x for missing arguments).

Methods (by class)

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

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

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

See Also

getNboot

Examples

# Dataset 'allOncoGeneLists' contains the result of the equivalence test between gene lists
# 'sanger' and 'atlas', at level 4 of the BP ontology:
data(eqTest_atlas.sanger_BP4)
eqTest_atlas.sanger_BP4
class(eqTest_atlas.sanger_BP4)
# This may correspond to the result of code like:
# eqTest_atlas.sanger_BP4 <- equivTestSorensen(
#   allOncoGeneLists[["sanger"]], allOncoGeneLists[["atlas"]],
#   geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
#   onto = "BP", GOLevel = 4, listNames = c("sanger", "atlas"))
#
# (But results may vary according to GO updating)

# Not a bootstrap test, first upgrade to a bootstrap test:
boot.sanger_atlas.BP.4 <- upgrade(eqTest_atlas.sanger_BP4, boot = TRUE)

#getEffNboot(eqTest_atlas.sanger_BP4)
getEffNboot(boot.sanger_atlas.BP.4)
getNboot(boot.sanger_atlas.BP.4)

# All pairwise equivalence tests at level 4 of the BP ontology
data(eqTest_all_BP4)
?eqTest_all_BP4
class(eqTest_all_BP4)
# This may correspond to a call like:
# eqTest_all_BP4 <- equivTestSorensen(allOncoGeneLists,
#                           geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
#                           onto = "BP", GOLevel = 4)
boot.BP.4 <- upgrade(eqTest_all_BP4, boot = TRUE)
getEffNboot(eqTest_all_BP4)
getEffNboot(boot.BP.4)
getNboot(boot.BP.4)
getEffNboot(boot.BP.4, simplify = FALSE)

# Bootstrap equivalence test iterated over all GO ontologies and levels 3 to 10.
# data(allEqTests)
# ?allEqTests
# class(allEqTests)
# This may correspond to code like:
# (By default, the tests are iterated over all GO ontologies and for levels 3 to 10)
# allEqTests <- allEquivTestSorensen(allOncoGeneLists,
#                                             geneUniverse = humanEntrezIDs,
#                                             orgPackg = "org.Hs.eg.db",
#                                             boot = TRUE)
# boot.allEqTests <- upgrade(allEqTests, boot = TRUE)
# Number of effective bootstrap replicates for all tests:
# getEffNboot(boot.allEqTests)
# getEffNboot(boot.allEqTests, simplify = FALSE)

# Number of effective bootstrap replicates for specific GO ontologies, levels or pairs
# of gene lists:
# getEffNboot(boot.allEqTests, GOLevel = "level 6")
# getEffNboot(boot.allEqTests, GOLevel = 6)
# getEffNboot(boot.allEqTests, GOLevel = seq.int(4,6))
# getEffNboot(boot.allEqTests, GOLevel = "level 6", simplify = FALSE)
# getEffNboot(boot.allEqTests, GOLevel = "level 6", listNames = c("waldman", "sanger"))
# getEffNboot(boot.allEqTests, GOLevel = seq.int(4,6), onto = "BP")
# getEffNboot(boot.allEqTests, GOLevel = seq.int(4,6), onto = "BP", simplify = FALSE)
# getEffNboot(boot.allEqTests, GOLevel = "level 6", onto = "BP",
#             listNames = c("atlas", "sanger"))
# getEffNboot(boot.allEqTests$BP$`level 4`)

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