GOSemSimDATA_class()

Class "GOSemSimDATA" This class stores IC and gene to go mapping for semantic similarity measurement

Description

Class "GOSemSimDATA" This class stores IC and gene to go mapping for semantic similarity measurement

GOSemSim_package()

Gene Ontology-based Sematic Similarity Measures

Description

Implementation of semantic similarity measures to estimate the functional similarities among Gene Ontology terms and gene products

Details

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.

list(list("ll"), list(" Package: ", list(), " GOSemSim", list(), " Type: ", list(), " Package", list(), " Version: ", list(), " ", "2.0.0", list(), " Date: ", list(), " 09-11-2012", list(), " biocViews:", list(), " 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", list(), " Depends:", list(), " ", list(), "

", "Imports: ", list(), " methods, AnnotationDbi, GO.db", list(), " ", "Suggests:", list(), " clusterProfiler, DOSE", list(), " ", "License: ", list(), " Artistic-2.0", list(), " "))

Author

Guangchuang Yu

Maintainer: Guangchuang Yu guangchuangyu@gmail.com

References

Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976--978, April 2010. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076

clusterSim()

Semantic Similarity Between Two Gene Clusters

Description

Given two gene clusters, this function calculates semantic similarity between them.

Usage

clusterSim(cluster1, cluster2, semData, measure = "Wang", drop = "IEA",
  combine = "BMA")

Arguments

Argument	Description
`cluster1`	A set of gene IDs.
`cluster2`	Another set of gene IDs.
`semData`	GOSemSimDATA object
`measure`	One of "Resnik", "Lin", "Rel", "Jiang" and "Wang" methods.
`drop`	A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations.
`combine`	One of "max", "avg", "rcmax", "BMA" methods, for combining semantic similarity scores of multiple GO terms associated with protein or multiple proteins assiciated with protein cluster.

Value

similarity

References

Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976--978, April 2010. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076

Examples

d <- godata('org.Hs.eg.db', ont="MF", computeIC=FALSE)
cluster1 <- c("835", "5261","241", "994")
cluster2 <- c("307", "308", "317", "321", "506", "540", "378", "388", "396")
clusterSim(cluster1, cluster2, semData=d, measure="Wang")

combineScores()

combining similarity matrix to similarity score

Description

Functions for combining similarity matrix to similarity score

Usage

combineScores(SimScores, combine)

Arguments

Argument	Description
`SimScores`	similarity matrix
`combine`	combine method

Value

similarity value

Author

Guangchuang Yu http://guangchuangyu.github.io

geneSim()

Semantic Similarity Between two Genes

Description

Given two genes, this function will calculate the semantic similarity between them, and return their semantic similarity and the corresponding GO terms

Usage

geneSim(gene1, gene2, semData, measure = "Wang", drop = "IEA",
  combine = "BMA")

Arguments

Argument	Description
`gene1`	Entrez gene id.
`gene2`	Another entrez gene id.
`semData`	GOSemSimDATA object
`measure`	One of "Resnik", "Lin", "Rel", "Jiang" and "Wang" methods.
`drop`	A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations.
`combine`	One of "max", "avg", "rcmax", "BMA" methods, for combining semantic similarity scores of multiple GO terms associated with protein or multiple proteins assiciated with protein cluster.

Value

list of similarity value and corresponding GO.

References

Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976--978, April 2010. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076

Examples

d <- godata('org.Hs.eg.db', ont="MF", computeIC=FALSE)
geneSim("241", "251", semData=d, measure="Wang")

goSim()

Semantic Similarity Between Two GO Terms

Description

Given two GO IDs, this function calculates their semantic similarity.

Usage

goSim(GOID1, GOID2, semData, measure = "Wang")

Arguments

Argument	Description
`GOID1`	GO ID 1.
`GOID2`	GO ID 2.
`semData`	GOSemSimDATA object
`measure`	One of "Resnik", "Lin", "Rel", "Jiang" and "Wang" methods.

Value

similarity

References

Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976--978, April 2010. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076

Examples

d <- godata('org.Hs.eg.db', ont="MF", computeIC=FALSE)
goSim("GO:0004022", "GO:0005515", semData=d, measure="Wang")

go_term_table()

Information content of GO terms

Description

These datasets are the information contents of GOterms.

References

Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976--978, April 2010. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076

godata()

godata

Description

prepare GO DATA for measuring semantic similarity

Usage

godata(OrgDb = NULL, keytype = "ENTREZID", ont, computeIC = TRUE)

Arguments

Argument	Description
`OrgDb`	OrgDb object
`keytype`	keytype
`ont`	one of 'BP', 'MF', 'CC'
`computeIC`	logical, whether computer IC

Value

GOSemSimDATA object

Author

Guangchuang Yu

infoContentMethod()

information content based methods

Description

Information Content Based Methods for semantic similarity measuring

Usage

infoContentMethod(ID1, ID2, method, godata)

Arguments

Argument	Description
`ID1`	Ontology Term
`ID2`	Ontology Term
`method`	one of "Resnik", "Jiang", "Lin" and "Rel".
`godata`	GOSemSimDATA object

Details

implemented for methods proposed by Resnik, Jiang, Lin and Schlicker.

Value

semantic similarity score

Author

Guangchuang Yu https://guangchuangyu.github.io

load_OrgDb()

load_OrgDb

Description

load OrgDb

Usage

load_OrgDb(OrgDb)

Arguments

Argument	Description
`OrgDb`	OrgDb object or OrgDb name

Value

OrgDb object

Author

Guangchuang Yu

mclusterSim()

Pairwise Semantic Similarities for a List of Gene Clusters

Description

Given a list of gene clusters, this function calculates pairwise semantic similarities.

Usage

mclusterSim(clusters, semData, measure = "Wang", drop = "IEA",
  combine = "BMA")

Arguments

Argument	Description
`clusters`	A list of gene clusters.
`semData`	GOSemSimDATA object
`measure`	One of "Resnik", "Lin", "Rel", "Jiang" and "Wang" methods.
`drop`	A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations.
`combine`	One of "max", "avg", "rcmax", "BMA" methods, for combining semantic similarity scores of multiple GO terms associated with protein or multiple proteins assiciated with protein cluster.

Value

similarity matrix

References

Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976--978, April 2010. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076

Examples

d <- godata('org.Hs.eg.db', ont="MF", computeIC=FALSE)
cluster1 <- c("835", "5261","241")
cluster2 <- c("578","582")
cluster3 <- c("307", "308", "317")
clusters <- list(a=cluster1, b=cluster2, c=cluster3)
mclusterSim(clusters, semData=d, measure="Wang")

mgeneSim()

Pairwise Semantic Similarity for a List of Genes

Description

Given a list of genes, this function calculates pairwise semantic similarities.

Usage

mgeneSim(genes, semData, measure = "Wang", drop = "IEA",
  combine = "BMA", verbose = TRUE)

Arguments

Argument	Description
`genes`	A list of entrez gene IDs.
`semData`	GOSemSimDATA object
`measure`	One of "Resnik", "Lin", "Rel", "Jiang" and "Wang" methods.
`drop`	A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations.
`combine`	One of "max", "avg", "rcmax", "BMA" methods, for combining semantic similarity scores of multiple GO terms associated with protein or multiple proteins assiciated with protein cluster.
`verbose`	show progress bar or not.

Value

similarity matrix

References

Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976--978, April 2010. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076

Examples

d <- godata('org.Hs.eg.db', ont="MF", computeIC=FALSE)
mgeneSim(c("835", "5261","241"), semData=d, measure="Wang")

mgoSim()

Semantic Similarity Between two GO terms lists

Description

Given two GO term sets, this function will calculate the semantic similarity between them, and return their semantic similarity

Usage

mgoSim(GO1, GO2, semData, measure = "Wang", combine = "BMA")

Arguments

Argument	Description
`GO1`	A set of go terms.
`GO2`	Another set of go terms.
`semData`	GOSemSimDATA object
`measure`	One of "Resnik", "Lin", "Rel", "Jiang" and "Wang" methods.
`combine`	One of "max", "avg", "rcmax", "BMA" methods, for combining semantic similarity scores of multiple GO terms associated with protein or multiple proteins assiciated with protein cluster.

Value

similarity

References

Yu et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics (Oxford, England), 26:7 976--978, April 2010. ISSN 1367-4803 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 PMID: 20179076

Examples

d <- godata('org.Hs.eg.db', ont="MF", computeIC=FALSE)
go1 <- c("GO:0004022", "GO:0004024", "GO:0004023")
go2 <- c("GO:0009055", "GO:0020037")
mgoSim("GO:0003824", go2, semData=d, measure="Wang")
mgoSim(go1, go2, semData=d, measure="Wang")

termSim()

termSim

Description

measuring similarities between two term vectors.

Usage

termSim(t1, t2, semData, method = c("Wang", "Resnik", "Rel", "Jiang",
  "Lin"))

Arguments

Argument	Description
`t1`	term vector
`t2`	term vector
`semData`	GOSemSimDATA object
`method`	one of "Wang", "Resnik", "Rel", "Jiang", and "Lin".

Details

provide two term vectors, this function will calculate their similarities.

Value

score matrix

Author

Guangchuang Yu http://guangchuangyu.github.io

wangMethod_internal()

wangMethod

Description

Method Wang for semantic similarity measuring

Usage

wangMethod_internal(ID1, ID2, ont = "BP")

Arguments

Argument	Description
`ID1`	Ontology Term
`ID2`	Ontology Term
`ont`	Ontology

Value

semantic similarity score

Author

Guangchuang Yu http://ygc.name

v3.9.0

bioconductor v3.9.0 GOSemSim

Link to this section Summary

Functions

Link to this section Functions

GOSemSimDATA_class()

Description

GOSemSim_package()

Description

Details

Seealso

Author

References

clusterSim()

Description

Usage

Arguments

Value

Seealso

References

Examples

combineScores()

Description

Usage

Arguments

Value

Author

geneSim()

Description

Usage

Arguments

Value

Seealso

References

Examples

goSim()

Description

Usage

Arguments

Value

Seealso

References

Examples

go_term_table()

Description

References

godata()

Description

Usage

Arguments

Value

Author

infoContentMethod()

Description

Usage

Arguments

Details

Value

Author

load_OrgDb()

Description

Usage

Arguments

Value

Author

mclusterSim()

Description

Usage

Arguments

Value

Seealso

References

Examples

mgeneSim()

Description

Usage

Arguments

Value

Seealso

References