ppiPre v1.6

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by Yue Deng

Predict protein-protein interactions based on functional and topological similarities.

This package provides functions for computing similarities between proteins based on their GO annotation, KEGG annotation and PPI network topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA and AA) to predict PPIs using an SVM classifier. Some internal functions are derived from R package GOSemSim authored by Guangchuang Yu.

Functions in ppiPre

Name Description
JaccardSim Compute Jaccard Index Between Two Nodes in PPI Network
SVMTrain Using Golden Standard Data Sets to Train an SVM Classifier
GOKEGGSimsFromFile GO- and KEGG- based Similarities Between two Genes
GOKEGGSims GO- and KEGG- based Similarities Between two Genes
KEGGSim KEGG Semantic Similarity Between two Genes
RASim Compute Resource Allocation Index Between Two Nodes in PPI Network
ComputeAllEvidences Compute the Biological and Topological Similarities Between Protein Pairs
ppiPre-internal Internal ppiPre objects
SVMPredict Predict false interactions using a training set
FNPre Predict false negative interactions based on topological similarities
TopologicSims Compute topological similarities from user input file
AASim Compute Adamic-Adar Index Between Two Nodes in PPI Network
ppiPre-package Predicting protein-protein interactions
TCSSGeneSim Topological Clustering Semantic Similarity(TCSS) Between two Genes
IntelliGOGeneSim IntelliGO Semantic Similarity Between two Genes
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Details

Type Package
Date 2015-01-25
License GPL-2
LazyLoad yes
NeedsCompilation no
Packaged 2015-01-29 10:13:00 UTC; Administrator
X-CRAN-Comment Earlier versions were removed as source code had been copied uncredited.
Repository CRAN
Date/Publication 2015-01-29 11:45:23

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