Multi Dimensional Gene Set Analysis.


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Documentation for package ‘mdgsa’ version 1.8.0

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annotFilter Checks and filters an annotation list.
annotList2mat Convert an annotation list into an annotation matrix.
annotMat2list Convert an annotation matrix into an annotation list.
getGOnames Get Gene Ontology names
getKEGGnames Get KEGG names
getOntology Get GO term Ontology
goLeaves Keep just leaf nodes from the Gene Ontology DAG.
indexTransform Transform ranking index distribution.
mdGsa Multi-Dimensional Gene Set Analysis.
mdPat Multi-Dimensional Gene Set Analysis Pattern Classification.
multidimensionalGsa Multi-Dimensional Gene Set Analysis.
multivariateGsa Multi-Dimensional Gene Set Analysis.
plotMdGsa Plot Multi-Dimensional Gene Set
propagateGO Propagate Gene Ontology annotation.
pval2index Transform p-values in into a ranking index.
revList Revert an annotation list.
splitOntologies Split an annotation list of GO terms by ontologies.
transferIndex Transfer a ranking index from regulatory elements, such as miRNAs, to genes.
univariateGsa Uni-Variate Gene Set Analysis.
uvGsa Uni-Variate Gene Set Analysis.
uvPat Uni-Variate Gene Set Analysis Pattern Classification.
uvSignif Filter significant terms in the univariate gene set analysis.