allEquivTestSorensen: Iterate 'equivTestSorensen' along the specified GO ontologies...

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

Iterate equivTestSorensen along the specified GO ontologies and GO levels

Description

Iterate equivTestSorensen along the specified GO ontologies and GO levels

Usage

allEquivTestSorensen(x, ...)

## S3 method for class 'list'
allEquivTestSorensen(
  x,
  d0 = 1/(1 + 1.25),
  conf.level = 0.95,
  boot = FALSE,
  nboot = 10000,
  check.table = TRUE,
  ontos = c("BP", "CC", "MF"),
  GOLevels = seq.int(3, 10),
  trace = TRUE,
  ...
)

## S3 method for class 'allTableList'
allEquivTestSorensen(
  x,
  d0 = 1/(1 + 1.25),
  conf.level = 0.95,
  boot = FALSE,
  nboot = 10000,
  check.table = TRUE,
  ontos,
  GOLevels,
  trace = TRUE,
  ...
)

Arguments

x	either an object of class "list" or an object of class "allTableList". In the first case, each of its elements must be a "character" vector of gene identifiers (e.g., ENTREZ).
...	extra parameters for function buildEnrichTable.
d0	equivalence threshold for the Sorensen-Dice dissimilarity, d. The null hypothesis states that d >= d0, i.e., inequivalence between the compared gene lists and the alternative that d < d0, i.e., equivalence or dissimilarity irrelevance (up to a level d0).
conf.level	confidence level of the one-sided confidence interval, a value between 0 and 1.
boot	boolean. If TRUE, the confidence interval and the test p-value are computed by means of a bootstrap approach instead of the asymptotic normal approach. Defaults to FALSE.
nboot	numeric, number of initially planned bootstrap replicates. Ignored if boot == FALSE. Defaults to 10000.
check.table	Boolean. If TRUE (default), argument x is checked to adequately represent a 2x2 contingency table (or an aggregate of them) or gene lists producing a correct table. This checking is performed by means of function nice2x2Table.
ontos	"character", GO ontologies to analyse. Defaults to c("BP", "CC", "MF").
GOLevels	"integer", GO levels to analyse inside each one of the GO ontologies.
trace	Logical. If TRUE (default), the (usually very time consuming) process of function allEquivTestSorensen is traced along the specified GO ontologies and levels.

Value

An object of class "AllEquivSDhtest". It is a list with as many components as GO ontologies have been analysed. Each of these elements is itself a list with as many components as GO levels have been analized. Finally, the elements of these lists are objects as generated by equivTestSorensen.list, i.e., objects of class "equivSDhtestList" containing pairwise comparisons between gene lists.

Methods (by class)

• allEquivTestSorensen(list): S3 method for class "list"

• allEquivTestSorensen(allTableList): S3 method for class "allTableList"

Examples

# Gene lists to be explored for enrichment:
data(allOncoGeneLists)

# Obtaining ENTREZ identifiers for the gene universe of humans:
library(org.Hs.eg.db)
humanEntrezIDs <- keys(org.Hs.eg.db, keytype = "ENTREZID")

# This example is highly time-consuming. It scans two GO ontologies and three
# GO levels inside them to perform the equivalence test.
# allEquivTestSorensen(allOncoGeneLists,
#                      geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db",
#                      ontos = c("MF", "BP"), GOLevels = seq.int(4,6))
# When the "ontos" and "GOLevels" arguments are not supplied, the function computes 
# by default every possible contingency table between the lists being compared for 
# the three ontologies (BP, CC, MF) and GO levels from 3 to 10. 
#
# Much faster:
# Object \code{allContTabs} of class "allTableList" contains all the pairwise contingency tables of
# joint enrichment for the gene lists in \code{allOncoGeneLists}, obtained along all three GO
# ontologies and along GO levels 3 to 10:
data(allContTabs)
tests <- allEquivTestSorensen(allContTabs, ontos = c("MF", "BP"), GOLevels = seq.int(4,6))
tests$BP$`level 5`
getPvalue(tests)

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