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Calculates a functional similarity measure between gene identifiers based on the pathways described on KEGG and REACTOME.

Important functions

  • pathSim(): Calculates the similarity between two pathways.

  • geneSim(): Calculates the similarity (based on pathSim) between two genes.

  • clusterSim(): Calculates the similarity between two clusters of genes by joining pathways of each gene.

  • clusterGeneSim(): Calculates the similarity between two clusters of genes by comparing the similarity between the genes of a cluster.

  • similarities(): Allows to combine the value of matrices of similarities.

  • conversions(): Two functions to convert similarity measures.

  • weighted(): Functions provided to combine similarities.

Author

Maintainer: Lluís Revilla Sancho lluis.revilla@gmail.com (ORCID)

Other contributors:

  • Pau Sancho-Bru (ORCID) [thesis advisor]

  • Juan José Salvatella Lozano (ORCID) [thesis advisor]