Package 'GOSemSim'

Title: GO-terms Semantic Similarity Measures
Description: The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.
Authors: Guangchuang Yu [aut, cre], Alexey Stukalov [ctb], Pingfan Guo [ctb], Chuanle Xiao [ctb], Lluís Revilla Sancho [ctb]
Maintainer: Guangchuang Yu <[email protected]>
License: Artistic-2.0
Version: 2.31.0
Built: 2024-06-30 02:43:24 UTC
Source: https://github.com/bioc/GOSemSim

Help Index

buildGOmap

Description

Addding indirect GO annotation

Usage

buildGOmap(TERM2GENE)

Arguments

TERM2GENE

data.frame with two or three columns of GO TERM, GENE and ONTOLOGY (optional)

Details

provided by a data.frame of GO TERM (column 1), GENE (column 2) and ONTOLOGY (optional) that describes GO direct annotation, this function will add indirect GO annotation of genes.

Value

data.frame, GO annotation with direct and indirect annotation

Author(s)

Yu Guangchuang

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

cluster1

A set of gene IDs.
cluster2

Another set of gene IDs.
semData

GOSemSimDATA object
measure

One of "Resnik", "Lin", "Rel", "Jiang", "TCSS" 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

See Also

goSim mgoSim geneSim mgeneSim mclusterSim

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")

combining similarity matrix to similarity score

Description

Functions for combining similarity matrix to similarity score

Usage

combineScores(SimScores, combine)

Arguments

SimScores

similarity matrix
combine

combine method

Value

similarity value

Author(s)

Guangchuang Yu http://guangchuangyu.github.io

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

gene1

Entrez gene id.
gene2

Another entrez gene id.
semData

GOSemSimDATA object
measure

One of "Resnik", "Lin", "Rel", "Jiang" "TCSS" 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

See Also

goSim mgoSim mgeneSim clusterSim mclusterSim

Examples

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

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

Description

prepare GO DATA for measuring semantic similarity

Usage

godata(
  OrgDb = NULL,
  annoDb = NULL,
  keytype = "ENTREZID",
  ont,
  computeIC = TRUE,
  processTCSS = FALSE,
  cutoff = NULL
)

Arguments

OrgDb

OrgDb object (will be removed in future, please use annoDb instead)
annoDb

GO annotation database, can be OrgDb or a data.frame contains three columns of 'GENE', 'GO' and 'ONTOLOGY'.
keytype

keytype
ont

one of 'BP', 'MF', 'CC'
computeIC

logical, whether computer IC
processTCSS

logical, whether to process TCSS
cutoff

cutoff of TCSS

Value

GOSemSimDATA object

Author(s)

Guangchuang Yu

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

Slots

keys

gene ID

ont

ontology

IC

IC data

geneAnno

gene to GO mapping

tcssdata

tcssdata

metadata

metadata

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

GOID1

GO ID 1.
GOID2

GO ID 2.
semData

GOSemSimDATA object
measure

One of "Resnik", "Lin", "Rel", "Jiang", "TCSS" 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

See Also

mgoSim geneSim mgeneSim clusterSim mclusterSim

Examples

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

information content based methods

Description

Information Content Based Methods for semantic similarity measuring

Usage

infoContentMethod(ID1, ID2, method, godata)

Arguments

ID1

Ontology Term
ID2

Ontology Term
method

one of "Resnik", "Jiang", "Lin" and "Rel", "TCSS".
godata

GOSemSimDATA object

Details

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

Value

semantic similarity score

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

load_OrgDb

Description

load OrgDb

Usage

load_OrgDb(OrgDb)

Arguments

OrgDb

OrgDb object or OrgDb name

Value

OrgDb object

Author(s)

Guangchuang Yu

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

clusters

A list of gene clusters.
semData

GOSemSimDATA object
measure

One of "Resnik", "Lin", "Rel", "Jiang", "TCSS" 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

See Also

goSim mgoSim geneSim mgeneSim clusterSim

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")

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

genes

A list of entrez gene IDs.
semData

GOSemSimDATA object
measure

One of "Resnik", "Lin", "Rel", "Jiang", "TCSS" 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

See Also

goSim mgoSim geneSim clusterSim mclusterSim

Examples

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

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

GO1

A set of go terms.
GO2

Another set of go terms.
semData

GOSemSimDATA object
measure

One of "Resnik", "Lin", "Rel", "Jiang", "TCSS" 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

See Also

goSim geneSim mgeneSim clusterSim mclusterSim

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")

read.blast2go

Description

given a BLAST2GO file, this function extracts the information from it and make it use for TERM2GENE.

Usage

read.blast2go(file, add_indirect_GO = FALSE)

Arguments

file

BLAST2GO file
add_indirect_GO

whether add indirect GO annotation

Value

a data frame with three columns: GENE, GO and ONTOLOGY

read.gaf

Description

parse GAF files

Usage

read.gaf(file, asis = FALSE, add_indirect_GO = FALSE)

parse_gff(file, asis = FALSE, add_indirect_GO = FALSE)

Arguments

file

GAF file
asis

logical, whether output the original contains of the file and only works if 'add_indirect_GO = FALSE'
add_indirect_GO

whether to add indirect GO annotation

Details

given a GAF file, this function extracts the information from it

Value

A data.frame. Original table if 'asis' works, otherwise contains 3 conlumns of 'GENE', 'GO' and 'ONTOLOGY'

determine the topological cutoff for TCSS method

Description

determine the topological cutoff for TCSS method

Usage

tcss_cutoff(
  OrgDb = NULL,
  keytype = "ENTREZID",
  ont,
  combine_method = "max",
  ppidata
)

Arguments

OrgDb

OrgDb object
keytype

keytype
ont

ontology : "BP", "MF", "CC"
combine_method

"max", "BMA", "avg", "rcmax", "rcmax.avg"
ppidata

A data.frame contains positive set and negative set. Positive set is PPI pairs that already verified. ppidata has three columns, column 1 and 2 are character, column 3 must be logical value:TRUE/FALSE.

Value

numeric, topological cutoff for given parameters

Examples

## Not run: 
    library(org.Hs.eg.db)
    library(STRINGdb)

    string_db <- STRINGdb$new(version = "11.0", species = 9606,
    score_threshold = 700)
    string_proteins <- string_db$get_proteins()

    #get relationship
    ppi <- string_db$get_interactions(string_proteins$protein_external_id)

    ppi$from <- vapply(ppi$from, function(e)
                       strsplit(e, "9606.")[[1]][2], character(1))
    ppi$to <- vapply(ppi$to, function(e)
                       strsplit(e, "9606.")[[1]][2], character(1))
    len <- nrow(ppi)

    #select length
    s_len <- 100
    pos_1 <- sample(len, s_len, replace = T)
    #negative set
    pos_2 <- sample(len, s_len, replace = T)
    pos_3 <- sample(len, s_len, replace = T)
    #union as ppidata
    ppidata <- data.frame(pro1 = c(ppi$from[pos_1], ppi$from[pos_2]),
     pro2 = c(ppi$to[pos_1], ppi$to[pos_3]),
     label = c(rep(TRUE, s_len), rep(FALSE, s_len)),
     stringsAsFactors = FALSE)

    cutoff <- tcss_cutoff(OrgDb = org.Hs.eg.db, keytype = "ENSEMBLPROT",
    ont = "BP", combine_method = "max", ppidata)

## End(Not run)

termSim

Description

measuring similarities between two term vectors.

Usage

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

Arguments

t1

term vector
t2

term vector
semData

GOSemSimDATA object
method

one of "Wang", "Resnik", "Rel", "Jiang", and "Lin", "TCSS".

Details

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

Value

score matrix

Author(s)

Guangchuang Yu http://guangchuangyu.github.io

wangMethod

Description

Method Wang for semantic similarity measuring

Usage

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

Arguments

ID1

Ontology Term
ID2

Ontology Term
ont

Ontology

Value

semantic similarity score

Author(s)

Guangchuang Yu http://ygc.name