getUpper: Access to the upper limit of the one-sided confidence...

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

Access to the upper limit of the one-sided confidence intervals for the Sorensen-Dice dissimilarity in 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 upper limits of the one-sided confidence intervals [0, dU] for the Sorensen-Dice dissimilarity.

Usage

getUpper(x, ...)

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

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

## S3 method for class 'AllEquivSDhtest'
getUpper(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

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

A numeric value, the upper limit of the one-sided confidence interval for 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 a single numeric value, the upper limit of the one-sided confidence interval for the Sorensen-Dice dissimilarity. 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 upper limit of the one-sided confidence intervals 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)

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

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

• getUpper(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)
getUpper(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)
getUpper(BP.4)
getUpper(BP.4, simplify = FALSE)

# Equivalence test iterated over all GO ontologies and levels 3 to 10:
data(cancerEquivSorensen)
?cancerEquivSorensen
class(cancerEquivSorensen)
# This may correspond to code like:
# (By default, the tests are iterated over all GO ontologies and for levels 3 to 10)
# cancerEquivSorensen <- allEquivTestSorensen(allOncoGeneLists,
#                                             geneUniverse = humanEntrezIDs,
#                                             orgPackg = "org.Hs.eg.db")
# All upper confidence limits for the Sorensen-Dice dissimilarities:
getUpper(cancerEquivSorensen)
getUpper(cancerEquivSorensen, simplify = FALSE)

# Upper confidence limits only for some GO ontologies, levels or pairs of gene lists:
getUpper(cancerEquivSorensen, GOLevel = "level 6")
getUpper(cancerEquivSorensen, GOLevel = 6)
getUpper(cancerEquivSorensen, GOLevel = seq.int(4,6))
getUpper(cancerEquivSorensen, GOLevel = "level 6", simplify = FALSE)
getUpper(cancerEquivSorensen, GOLevel = "level 6", listNames = c("waldman", "sanger"))
getUpper(cancerEquivSorensen, GOLevel = seq.int(4,6), onto = "BP")
getUpper(cancerEquivSorensen, GOLevel = seq.int(4,6), onto = "BP", simplify = FALSE)
getUpper(cancerEquivSorensen, GOLevel = "level 6", onto = "BP",
         listNames = c("waldman", "sanger"))
getUpper(cancerEquivSorensen$BP$`level 4`)

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