hpSetCompSummary: Global semantic similarity between 2 HP sets

In PCAN: Phenotype Consensus ANalysis (PCAN)

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),]

Example output

Loading required package: BiocParallel
        db     id               name
10189 OMIM 612285 Joubert syndrome 9
    entrez                                    name symbol
128  57545 coiled-coil and C2 domain containing 2A CC2D2A
[1] 1.684727
               id                    name
1817   HP:0002419 Molar tooth sign on MRI
1817.1 HP:0002419 Molar tooth sign on MRI

PCAN documentation built on Nov. 8, 2020, 6:47 p.m.