We add the following function:
In addition:
We have updated the buildEnrichedTable and allBuildEnrichedTable functions. They now uses the outcomes of enrichedIn to build the contingency table. During the conducted tests, the speed of the procedure for generating contingency tables increased by a factor of six compared to the previous version.
Furthermore, we have included the showEnrichedIn argument in these functions. This is a boolean argument. If the argument is TRUE, in addition to the enrichment contingency table, the function saves a matrix in the global environment, which contains the cross table of the enriched and non-enriched GO terms vs the names of the gene lists generated with the enrichedIn function. This matrix is stored under the name of "enrichedIn_" followed by the name of the ontology and the level being analysed. An object will be produced for every scenario if there are several levels and ontologies.
We add the vignette "irrelevance-threshold_Matrix_Dissimilarities." This vignette illustrates calculating, visualizing, and interpreting the irrelevance-threshold matrix of dissimilarities D. This matrix provides dissimilarities between pairs of compared lists. These dissimilarities are not only a descriptive measure but also based on the irrelevance threshold determining whether two lists are equivalent. So, this dissimilarity measure between the two lists is directly associated with their declaration of equivalence.
The matrix D can be represented in interpretable statistic graphs such as dendrograms or biplots, which help to visualize the formation of groups containing equivalent lists. Furthermore, interpreting the biplot dimensions gives us the biological functions responsible for the equivalence between lists.
We add the following functions:
In addition: