Changes in version 1.7.0
We add the following function:
- enrichedIn: This function generates a binary matrix in which the
rows represent GO terms, and the columns represent lists. The matrix
uses the values TRUE or FALSE to indicate whether each GO term is
enriched or not for each list.
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.
Changes in version 1.3.0
We add the following functions:
- allBuildEnrichTable: This function produces k(k–1)/2 contingency
tables by comparing all possible pairs of feature lists using the
provided GO ontologies and GO levels.
- allEquivTestSorensen: This function computes the k(k–1)/2
equivalence tests by comparing all possible pairs of feature lists
using the provided GO ontologies and GO levels.
- sorenThreshold: This function applies an algorithm to compute the
irrelevance-threshold matrix of dissimilarities for a specific
ontology and GO level.
- allSorenThreshold: This function iterates sorenThreshold along the
specified GO ontologies and GO levels
- hclustThreshold: This function plots a dendrogram for a specific
ontology and GO level based on the irrelevance-threshold matrix of
dissimilarities..
- allHclustThreshold: This function iterates hclustThreshold along the
specified GO ontologies and GO levels
In addition:
- We enhance the vignette "An introduction to the goSorensen package"
by incorporating the newly introduced functions and updating the
example results with the latest version of Bioconductor.
Changes in version 1.2.0
- Added some results (allTabsBP.4 object) about computed crosstabs for
all possible list pairs in allOncoGeneLists for BP ontology, level 4
Changes in version 1.1.0
- This is the first version submitted to review. There are currently
no updates.