Changes in version 1.3.0
We add the following functions
- allBuildEnrichTable: Given k lists of genes, it generates the
k(k–1)/2 contingency tables of joint enrichment for all possible
pairs of lists.
- allEquivTestSorensen: Accepts the objects created with
allBuildEnrichTable as its first argument and quickly obtains the
k(k–1)/2 equivalence tests.
- sorenThreshold: Implements an algorithm allowing the computation of
the “equivalence threshold” dissimilarities matrix for all the
k(k–1)/2 tests. According to what is indicated in the arguments,
the results of this function are stored in a matrix for a specific
ontology and level or a list with a matrix for more than one
ontology and/or level.
- hclustThreshold: Generates an object of class "hclust". For a
specific ontology and level, plots a dendrogram where all the
k(k–1)/2 comparisons are joined at the height of their respective
"equivalence threshold" dissimilarity.
- allHclustThreshold: Performs the same calculations as
hclustThreshold but for the specified GO ontologies and levels (all
three ontologies PB, MF, and CC and levels from 2 to 10 by default)
In addition:
- We improve the vignette "An introduction to the goSorensen package"
by implementing the new functions mentioned above and updating the
results of the examples with the results of 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.