R/GOSemSim-package.R

In GOSemSim: GO-terms Semantic Similarity Measures

##'Gene Ontology-based Sematic Similarity Measures
##'
##'Implementation of semantic similarity measures to estimate the functional
##'similarities among Gene Ontology terms and gene products
##'
##'Quantitative measure of functional similarities among gene products is
##'important for post-genomics study. and widely used in gene function
##'prediction, cluster analysis and pathway modeling.  This package is designed
##'to estimate the GO terms' and genes' semantic similarities.  Implemented five
##'methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.
##'Support many species, including Anopheles, Arabidopsis, Bovine, Canine,
##'Chicken, Chimp, E coli strain K12 and strain Sakai, Fly, Human, Malaria,
##'Mouse, Pig, Rhesus, Rat, Worm, Xenopus, Yeast, Zebrafish.
##'
##'\tabular{ll}{ Package: \tab GOSemSim\cr Type: \tab Package\cr Version: \tab
##'2.0.0\cr Date: \tab 09-11-2012\cr biocViews:\tab GO, Clustering, Pathways,
##'Anopheles_gambiae, Arabidopsis_thaliana, Bos_taurus, Caenorhabditis_elegans,
##'Canis_familiaris, Danio_rerio, Drosophila_melanogaster, Escherichia_coli,
##'Gallus_gallus, Homo_sapiens, Mus_musculus, Pan_troglodytes,
##'Plasmodium_falciparum, Rattus_norvegicus, Saccharomyces_cerevisiae,
##'Streptomyces_coelicolor, Sus_scrofa, Xenopus_laevis\cr Depends:\tab \cr
##'Imports: \tab methods, AnnotationDbi, GO.db\cr
##'Suggests:\tab clusterProfiler, DOSE\cr
##'License: \tab Artistic-2.0\cr }
##'
##'@name GOSemSim-package
##'@aliases GOSemSim-package GOSemSim
##'@docType package
##'@author Guangchuang Yu
##'
##'Maintainer: Guangchuang Yu <guangchuangyu@@gmail.com>
##'@seealso \code{\link{goSim}} \code{\link{mgoSim}} \code{\link{geneSim}}
##'\code{\link{mgeneSim}} \code{\link{clusterSim}} \code{\link{mclusterSim}}
##'@references Yu et al. (2010) GOSemSim: an R package for measuring semantic
##'similarity among GO terms and gene products \emph{Bioinformatics} (Oxford,
##'England), 26:7 976--978, April 2010. ISSN 1367-4803
##'\url{http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976}
##'PMID: 20179076
##'@keywords package
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##'Information content of GO terms
##'
##'These datasets are the information contents of GOterms.
##'
##'
##'@name go_term_table
##'@aliases GO gotbl
##'@docType data
##'@references Yu et al. (2010) GOSemSim: an R package for measuring semantic
##'similarity among GO terms and gene products \emph{Bioinformatics} (Oxford,
##'England), 26:7 976--978, April 2010. ISSN 1367-4803
##'\url{http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976}
##'PMID: 20179076
##'@keywords datasets
NULL