Smaller bug and typo fixes
Fixed the bug that the getGenes() function would set all gene names to all
caps which lead to the inability to download the correct PPI information for
species like mouse. Also renamed the function to prepareGenesetData() to
reflect more accurately its behavior.
Updated the default version used in the getId() and getStringDB() to 12.0,
the current version of the String database.
Fixed the broken zoom feature in the Optional Filtering Step in the Data Input panel. Additionally added a column Description to the table of zoomed gene sets to facilitate interpretation.
Fixed that the clustering will now be reset whenever a new score is calculated.
Updated the checkInclusion() function to drastically reduce runtime.
Fixed the error that the value of alpha would not be properly pass to all the
sub function used by the getpMMMatrix() function.
Replaced all occurrences of PMM with pMM to match the notation of the original publication.
Replaced the kNN clustering algorithm with PAM (partitioning around mendoids) as this seems to be more suitable for enrichment data represented by distance scores.
Renamed the goSimilarity() function to goDistance() to better indicated
that this is a distance rather than a similarity score. Also scaled all
scores to the [0, 1] interval.
Fixed the normalization function in the getKappaDistanceMatrix() function.
Changed the implementation of the Louvain clustering algorithm to use a weighted graph now. The graph is weighted by the distance scores between gene sets.
Added GeneTonicList as a possible input object for GeDi. Now GeDi is directly
compatible with GeneTonic.
col_name_genesets and col_name_genes as parameter to the GeDi() main app to allow users to specify the relevant column names upon executing the command| with || and similar)globalVariables()for loops to avoid unhealthy growing of vectors/matricesSerialParam() to
avoid unexpected behaviors