R/gosorensen.R

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
#'
#' 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.
#'
#' gosorensen package provides the following functions:
#' \describe{
#'   \item{enrichedIn}{Build a cross-tabulation of enriched and non-enriched GO terms vs. gene lists}
#'   \item{buildEnrichTable}{Build an enrichment contingency table from two or more gene lists}
#'   \item{allBuildEnrichTable}{Iterate 'buildEnrichTable' along the specified GO ontologies and GO levels}
#'   \item{nice2x2Table}{Check for validity an enrichment contingency table}
#'   \item{dSorensen}{Compute the Sorensen-Dice dissimilarity}
#'   \item{seSorensen}{Standard error estimate of the sample Sorensen-Dice dissimilarity}
#'   \item{duppSorensen}{Upper limit of a one-sided confidence interval (0,dUpp] for the population dissimilarity}
#'   \item{equivTestSorensen}{Equivalence test between two gene lists, based on the Sorensen-Dice dissimilarity}
#'   \item{allEquivTestSorensen}{Iterate equivTestSorensen along GO ontologies and GO levels}
#'   \item{getDissimilarity, getPvalue, getSE, getTable, getUpper, getNboot, getEffNboot}{Accessor functions to some fields of an equivalence test result}
#'   \item{upgrade}{Updating the result of an equivalence test, e.g., changing the equivalence limit}
#'   \item{sorenThreshold}{For a given level (2, 3, ...) in a GO ontology (BP, MF or CC), compute the equivalence threshold dissimilarity matrix.}
#'   \item{allSorenThreshold}{Iterate 'sorenThreshold' along the specified GO ontologies and GO levels.}
#'   \item{hclustThreshold}{From a Sorensen-Dice threshold dissimilarity matrix, generate an object of class "hclust"}
#'   \item{allHclustThreshold}{Iterate 'hclustThreshold' along the specified GO ontologies and GO levels}
#'   \item{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.
#'
#' @docType package
#' @name gosorensen
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