hpSetCompSummary {PCAN} | R Documentation

## Global semantic similarity between 2 HP sets

### Description

This function summarize the comparison of 2 sets of HP terms

### Usage

    hpSetCompSummary(hpSetComp, method = c("bma", "bm", "average"),
      direction = c("symSim", "r", "c"))

### Arguments

`hpSetComp` | a matrix of semantic similarities between couples of HP terms
`method` | "bma" (Best Match Average): the average of the best matches on rows or columns (see direction param). "bm": the maximum value. "average": the average of the whole matrix.
`direction` | taken into account only if method="bma". "r": best match per row. "c": best match per column. "symSim" (symmetric semantic similarity): average of calls with "r" and "c"

### Value

A numeric value corresponding to the semantic similarity of the 2 HP sets

### Author(s)

Patrice Godard

### See Also

`compareHPSets`

### Examples

    ## Prerequisite
    data(geneByHp, hp_descendants, package="PCAN")
    geneByHp <- unstack(geneByHp, entrez~hp)
    ic <- computeHpIC(geneByHp, hp_descendants)

    ###########################################
    ## Use case: comparing a gene and a disease
    data(traitDef, geneDef, hp_ancestors, hpDef, package="PCAN")
    omim <- "612285"
    traitDef[which(traitDef$id==omim),]
    entrez <- "57545"
    geneDef[which(geneDef$entrez==entrez),]
    ## Get HP terms associated to the disease
    data(hpByTrait, package="PCAN")
    hpOfInterest <- hpByTrait$hp[which(hpByTrait$id==omim)]

    ## Get HP terms associated to the gene
    hpByGene <- unstack(stack(geneByHp), ind~values)
    geneHps <- hpByGene[[entrez]]
    ## Comparison of the two sets of HP terms
    compMat <- compareHPSets(
        hpSet1=geneHps, hpSet2=hpOfInterest,
        IC=ic,
        ancestors=hp_ancestors,
        method="Resnik",
        BPPARAM=SerialParam()
    )
    ## Get the symmetric semantic similarity score
    hpSetCompSummary(compMat, method="bma", direction="symSim")
    bm <- hpSetCompBestMatch(compMat, "b")
    hpDef[match(c(bm$compared, bm$candidate), hpDef$id),]

[Package PCAN version 1.17.0 Index]