In this updated version, the package allows enrichment analysis and downstream comparisons without restricting the computation to a specific GO level. By setting the arguments GOLevel = NULL or GOLevels = NULL, users can work directly with all GO terms in the selected ontology.
Additionally, the main functions now include the keyType argument, allowing users to specify the type of gene identifiers (e.g., ENTREZID, SYMBOL, etc.) used in the analysis, improving flexibility and compatibility with different genes' ID.
This new functionality has been incorporated into the following functions:
In addition:
In this updated version, unless the user specifies otherwise in the onlyEnriched argument of the enrichedIn function, the enrichment matrix of GO terms includes only those terms that are enriched in at least one of the lists being compared, excluding all terms that are not enriched in any of the lists. This optimization significantly reduces computation times for enrichment analysis compared to previous versions, such as when generating enrichment contingency tables using buildEnrichTable.
Additionally, with the latest versions of Bioconductor and its updated packages, we have revised the naming conventions and outputs for results obtained from the primary goSorensen functions. These changes are summarized in two new bullet points, offering clearer guidance and improved usability for package users compared to earlier versions.
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: