R/703-calcProtGOSim.R

In nanxstats/Rcpi: Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

.orgdb = c(
    'anopheles' = 'org.Ag.eg.db',
    'arabidopsis' = 'org.At.tair.db',
    'bovine' = 'org.Bt.eg.db',
    'canine' = 'org.Cf.eg.db',
    'chicken' = 'org.Gg.eg.db',
    'chimp' = 'org.Pt.eg.db',
    'coelicolor' = 'org.Sco.eg.db',
    'ecolik12' = 'org.EcK12.eg.db',
    'ecsakai' = 'org.EcSakai.eg.db',
    'fly' = 'org.Dm.eg.db',
    'human' = 'org.Hs.eg.db',
    'malaria' = 'org.Pf.plasmo.db',
    'mouse' = 'org.Mm.eg.db',
    'pig' = 'org.Ss.eg.db',
    'rat' = 'org.Rn.eg.db',
    'rhesus' = 'org.Mmu.eg.db',
    'worm' = 'org.Ce.eg.db',
    'xenopus' = 'org.Xl.eg.db',
    'yeast' = 'org.Sc.sgd.db',
    'zebrafish' = 'org.Dr.eg.db'
)

.calcgoPairSim = function(twoid, golist, godb, measure, combine) {

    id1 = twoid[1]
    id2 = twoid[2]

    if ( all(golist[[id1]] == '') | all(golist[[id2]] == '') ) {

        sim = 0L

    } else {

        id1good = 1:length(golist[[id1]])
        id2good = 1:length(golist[[id2]])

        gid1 = as.character(golist[[id1]][id1good])
        gid2 = as.character(golist[[id2]][id2good])

        res = try(suppressWarnings(GOSemSim::mgoSim(
            gid1, gid2, semData = godb, measure = measure, combine = combine
        )),
        silent = TRUE)

        if ( is.numeric(res) ) {
            sim = res
        } else {
            sim = 0L
        }

    }

    sim

}

#' Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity
#'
#' Protein Sequence Similarity Calculation based on Gene Ontology (GO) Similarity
#'
#' This function calculates
#' protein sequence similarity based on Gene Ontology (GO) similarity.
#'
#' @param golist A character vector, each component contains
#' a character vector of GO terms or one Entrez Gene ID.
#' @param type Input type of \code{golist}, \code{'go'} for GO Terms,
#' \code{'gene'} for gene ID.
#' @param ont Default is \code{'MF'}, could be one of
#' \code{'MF'}, \code{'BP'}, or \code{'CC'} subontologies.
#' @param organism Default is \code{'human'}, could be one of
#' \code{'anopheles'}, \code{'arabidopsis'}, \code{'bovine'}, \code{'canine'},
#' \code{'chicken'}, \code{'chimp'}, \code{'coelicolor'}, \code{'ecolik12'},
#' \code{'ecsakai'}, \code{'fly'}, \code{'human'}, \code{'malaria'},
#' \code{'mouse'}, \code{'pig'}, \code{'rat'}, \code{'rhesus'},
#' \code{'worm'}, \code{'xenopus'}, \code{'yeast'} or \code{'zebrafish'}.
#' @param measure Default is \code{'Resnik'}, could be one of
#' \code{'Resnik'}, \code{'Lin'}, \code{'Rel'}, \code{'Jiang'} or \code{'Wang'}.
#' @param combine Default is \code{'BMA'}, could be one of
#' \code{'max'}, \code{'average'}, \code{'rcmax'} or \code{'BMA'}
#' for combining semantic similarity scores of multiple GO terms
#' associated with protein.
#' @return A \code{n} x \code{n} similarity matrix.
#'
#' @seealso See \code{\link{calcTwoProtGOSim}} for calculating the
#' GO semantic similarity between two groups of GO terms or two Entrez gene IDs.
#' See \code{\link{calcParProtSeqSim}} for paralleled protein similarity
#' calculation based on sequence alignment.
#'
#' @export calcParProtGOSim
#'
#' @examples
#' # By GO Terms
#' go1 = c('GO:0005215', 'GO:0005488', 'GO:0005515', 'GO:0005625', 'GO:0005802', 'GO:0005905')  # AP4B1
#' go2 = c('GO:0005515', 'GO:0005634', 'GO:0005681', 'GO:0008380', 'GO:0031202')  # BCAS2
#' go3 = c('GO:0003735', 'GO:0005622', 'GO:0005840', 'GO:0006412')  # PDE4DIP
#' glist = list(go1, go2, go3)
#' \donttest{calcParProtGOSim(glist, type = 'go', ont = 'CC', measure = 'Wang')}
#'
#' # By Entrez gene id
#' genelist = list(c('150', '151', '152', '1814', '1815', '1816'))
#' \donttest{calcParProtGOSim(genelist, type = 'gene', ont = 'BP', measure = 'Wang')}

calcParProtGOSim = function(
    golist, type = c('go', 'gene'),
    ont = c('MF', 'BP', 'CC'), organism = 'human',
    measure = 'Resnik', combine = 'BMA') {

    type = match.arg(type)
    ont = match.arg(ont)

    godb = suppressMessages(GOSemSim::godata(OrgDb = .orgdb[organism], ont = ont, computeIC = TRUE))

    if ( type == 'gene' ) {
        gosimmat = GOSemSim::mgeneSim(
            unlist(golist), godb,
            measure = measure, combine = combine, verbose = FALSE)
    }

    if ( type == 'go' ) {

        # generate lower matrix index
        idx = combn(1:length(golist), 2)

        # input is all pair combination
        gosimlist = vector('list', ncol(idx))

        for ( i in 1:ncol(idx) ) {
            gosimlist[[i]] = .calcgoPairSim(
                rev(idx[, i]), golist = golist, godb,
                measure = measure, combine = combine)
        }

        # convert list to matrix
        gosimmat = matrix(0, length(golist), length(golist))
        for (i in 1:length(gosimlist)) gosimmat[idx[2, i], idx[1, i]] = gosimlist[[i]]
        gosimmat[upper.tri(gosimmat)] = t(gosimmat)[upper.tri(t(gosimmat))]
        diag(gosimmat) = 1

    }

    gosimmat

}

#' Protein Similarity Calculation based on Gene Ontology (GO) Similarity
#'
#' Protein Similarity Calculation based on Gene Ontology (GO) Similarity
#'
#' This function calculates the Gene Ontology (GO) similarity
#' between two groups of GO terms or two Entrez gene IDs.
#'
#' @param id1 A character vector. length > 1: each element is a GO term;
#' length = 1: the Entrez Gene ID.
#' @param id2 A character vector. length > 1: each element is a GO term;
#' length = 1: the Entrez Gene ID.
#' @param type Input type of id1 and id2, \code{'go'} for GO Terms,
#' \code{'gene'} for gene ID.
#' @param ont Default is \code{'MF'}, could be one of
#' \code{'MF'}, \code{'BP'}, or \code{'CC'} subontologies.
#' @param organism Default is \code{'human'}, could be one of
#' \code{'anopheles'}, \code{'arabidopsis'}, \code{'bovine'}, \code{'canine'},
#' \code{'chicken'}, \code{'chimp'}, \code{'coelicolor'}, \code{'ecolik12'},
#' \code{'ecsakai'}, \code{'fly'}, \code{'human'}, \code{'malaria'},
#' \code{'mouse'}, \code{'pig'}, \code{'rat'}, \code{'rhesus'},
#' \code{'worm'}, \code{'xenopus'}, \code{'yeast'} or \code{'zebrafish'}.
#' @param measure Default is \code{'Resnik'}, could be one of
#' \code{'Resnik'}, \code{'Lin'}, \code{'Rel'}, \code{'Jiang'} or \code{'Wang'}.
#' @param combine Default is \code{'BMA'}, could be one of
#' \code{'max'}, \code{'average'}, \code{'rcmax'} or \code{'BMA'}
#' for combining semantic similarity scores of multiple GO terms
#' associated with protein.
#' @return A n x n matrix.
#'
#' @seealso See \code{\link{calcParProtGOSim}} for
#' protein similarity calculation based on
#' Gene Ontology (GO) semantic similarity.
#' See \code{\link{calcParProtSeqSim}} for paralleled protein similarity
#' calculation based on sequence alignment.
#'
#' @export calcTwoProtGOSim
#'
#' @examples
#' # By GO terms
#' go1 = c("GO:0004022", "GO:0004024", "GO:0004023")
#' go2 = c("GO:0009055", "GO:0020037")
#' \donttest{calcTwoProtGOSim(go1, go2, type = 'go', ont = 'MF', measure = 'Wang')}
#'
#' # By Entrez gene id
#' gene1 = '241'
#' gene2 = '251'
#' \donttest{calcTwoProtGOSim(gene1, gene2, type = 'gene', ont = 'CC', measure = 'Lin')}

calcTwoProtGOSim = function(
    id1, id2, type = c('go', 'gene'),
    ont = c('MF', 'BP', 'CC'), organism = 'human',
    measure = 'Resnik', combine = 'BMA') {

    type = match.arg(type)
    ont = match.arg(ont)

    godb = suppressMessages(GOSemSim::godata(OrgDb = .orgdb[organism], ont = ont, computeIC = TRUE))

    if ( type == 'go' ) {
        sim = GOSemSim::mgoSim(
            id1, id2,
            semData = godb,
            measure = measure, combine = combine)
    }

    if ( type == 'gene' ) {
        sim = GOSemSim::geneSim(
            id1, id2,
            semData = godb,
            measure = measure, combine = combine)
        if ("geneSim" %in% names(sim)) sim = sim$geneSim
    }

    sim

}