upgrade: Update the result of a Sorensen-Dice equivalence test.

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

Update the result of a Sorensen-Dice equivalence test.

Description

Recompute the test (or tests) from an object of class "equivSDhtest", "equivSDhtestList" or "AllEquivSDhtest" (i.e.,the output of functions "equivTestSorensen" or "allEquivTestSorensen"). Using the same table or tables of enrichment frequencies in 'x', obtain again the result of the equivalence test for new values of any of the parameters d0 or conf.level or boot or nboot or check.table.

Usage

upgrade(x, ...)

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

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

## S3 method for class 'AllEquivSDhtest'
upgrade(x, ...)

Arguments

x	an object of class "equivSDhtest", "equivSDhtestList" or "AllEquivSDhtest".
...	any valid parameters for function "equivTestSorensen" for its interface "table", to recompute the test(s) according to these parameters.

Value

An object of the same class than x.

Methods (by class)

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

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

• upgrade(AllEquivSDhtest): S3 method for class "allEquivSDhtest"

Examples

# Result of the equivalence test between gene lists 'waldman' and 'atlas', in dataset
# 'allOncoGeneLists', 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:
# data(allOncoGeneLists)
# library(org.Hs.eg.db)
# humanEntrezIDs <- keys(org.Hs.eg.db, keytype = "ENTREZID")
# waldman_atlas.BP.4 <- equivTestSorensen(
#   allOncoGeneLists[["waldman"]], allOncoGeneLists[["atlas"]],
#   geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
#   onto = "BP", GOLevel = 4, listNames = c("waldman", "atlas"))
upgrade(waldman_atlas.BP.4, d0 = 1/(1 + 10/9)) # d0 = 0.4737
upgrade(waldman_atlas.BP.4, d0 = 1/(1 + 2*1.25)) # d0 = 0.2857
upgrade(waldman_atlas.BP.4, d0 = 1/(1 + 2*1.25), conf.level = 0.99)

# 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:
# data(allOncoGeneLists)
# library(org.Hs.eg.db)
# humanEntrezIDs <- keys(org.Hs.eg.db, keytype = "ENTREZID")
# BP.4 <- equivTestSorensen(allOncoGeneLists,
#                           geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
#                           onto = "BP", GOLevel = 4)
upgrade(BP.4, d0 = 1/(1 + 2*1.25)) # d0 = 0.2857

data(cancerEquivSorensen)
?cancerEquivSorensen
class(cancerEquivSorensen)
upgrade(cancerEquivSorensen, d0 = 1/(1 + 2*1.25)) # d0 = 0.2857

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