cont_all_BP4: Example of the output produced by the function...

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

Example of the output produced by the function buildEnrichTable. It contains the enrichment contingency tables for all the lists from allOncoGeneLists at level 4 of ontology BP.

Description

Given 7 lists contained in allOncoGeneLists, this object contains the 7(6)/2 = 21 possible enrichment contingency tables to compare all possible pairs of lists. Each contingency 2x2 table contains the number of joint enriched GO terms (TRUE-TRUE); the number of GO terms enriched only in one list but not in the other one (FALSE-TRUE and TRUE-FALSE); and the number of GO terms not enriched in either of the two lists.

An important attribute of this object is enriched, which contains the enrichment matrix obtained using the function enrichedIn. Actually, the contingency tables in this object are derived from cross-frequency tables created between pairs of lists, which are located as columns in this enrichment matrix.

Usage

data(cont_all_BP4)

Format

An exclusive object from goSorensen of the class "tableList"

Details

Consider this object only as an illustrative example, which is valid exclusively for the data allOncoGeneLists contained in this package. Note that gene lists, GO terms, and Bioconductor may change over time. The current version of these results were generated with Bioconductor version 3.20.

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