gosorensen: gosorensen: A package for making inference on gene lists...

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

gosorensen: A package for making inference on gene lists based on the Sorensen-Dice dissimilarity

Description

Given two lists of genes, and a set of Gene Ontology (GO) items (e.g., all GO items in a given level of a given GO ontology) one may explore some aspects of their biological meaning by constructing a 2x2 contingency table, the cross-tabulation of: number of these GO items non-enriched in both gene lists (n00), items enriched in the first list but not in the second one (n10), items non-enriched in the first list but enriched in the second (n10) and items enriched in both lists (n11). Then, one may express the degree of similarity or dissimilarity between the two lists by means of an appropriate index computed on these frequency tables of concordance or non-concordance in GO items enrichment. In our opinion, an appropriate index is the Sorensen-Dice index which ignores the double negatives n00: if the total number of candidate GO items under consideration grows (e.g., all items in a deep level of an ontology) likely n00 will also grow artificially. On the other hand, intuitively the degree of similarity between both lists must be directly related to the degree of concordance in the enrichment, n11.

Details

gosorensen package provides the following functions:

enrichedIn

Build a cross-tabulation of enriched and non-enriched GO terms vs. gene lists

buildEnrichTable

Build an enrichment contingency table from two or more gene lists

allBuildEnrichTable

Iterate 'buildEnrichTable' along the specified GO ontologies and GO levels

nice2x2Table

Check for validity an enrichment contingency table

dSorensen

Compute the Sorensen-Dice dissimilarity

seSorensen

Standard error estimate of the sample Sorensen-Dice dissimilarity

duppSorensen

Upper limit of a one-sided confidence interval (0,dUpp] for the population dissimilarity

equivTestSorensen

Equivalence test between two gene lists, based on the Sorensen-Dice dissimilarity

allEquivTestSorensen

Iterate equivTestSorensen along GO ontologies and GO levels

getDissimilarity, getPvalue, getSE, getTable, getUpper, getNboot, getEffNboot

Accessor functions to some fields of an equivalence test result

upgrade

Updating the result of an equivalence test, e.g., changing the equivalence limit

sorenThreshold

For a given level (2, 3, ...) in a GO ontology (BP, MF or CC), compute the equivalence threshold dissimilarity matrix.

allSorenThreshold

Iterate 'sorenThreshold' along the specified GO ontologies and GO levels.

hclustThreshold

From a Sorensen-Dice threshold dissimilarity matrix, generate an object of class "hclust"

allHclustThreshold

Iterate 'hclustThreshold' along the specified GO ontologies and GO levels

pruneClusts

Remove all NULL or unrepresentable as a dendrogram "equivClustSorensen" elements in an object of class "equivClustSorensenList"

All these functions are generic, adequate for different (S3) classes representing the before cited GO term enrichment cross-tabulations.

Author(s)

Maintainer: Pablo Flores [e-mail] (ORCID)

Authors:

• Jordi Ocana (ORCID) [contributor]

Other contributors:

• Alexandre Sanchez-Pla (ORCID) [contributor]

• Miquel Salicru (ORCID) [contributor]

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