calcHpSim: Compare HP terms based on semantic similarity

In PCAN: Phenotype Consensus ANalysis (PCAN)

Description

This function compares 2 HP terms based on provided Information Content and ancestors

Usage

calcHpSim(term1, term2, method = c("Resnik"), IC, ancestors)

Arguments

term1	one of the HP term to compare
term2	the other HP term to compare
method	the method for computing semantic simalirity (default: "Resnik" returns the IC of the MICA: Most Informative common ancestor)
IC	a named vector of Information Content by HP term
ancestors	a named list of ancestors by HP term

Value

A numeric value

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)

## Compute similarity between different couples of HP terms
data(hp_ancestors, hpDef, package="PCAN")
hp1 <- "HP:0000518"
hp2 <- "HP:0030084"
hp3 <- "HP:0002119"
hp4 <- "HP:0001305"
hpDef[which(hpDef$id %in% c(hp1, hp2)), 1:2]
calcHpSim(hp1, hp2, IC=ic, ancestors=hp_ancestors)
hpDef[which(hpDef$id %in% c(hp2, hp3)), 1:2]
calcHpSim(hp2, hp3, IC=ic, ancestors=hp_ancestors)
hpDef[which(hpDef$id %in% c(hp2, hp4)), 1:2]
calcHpSim(hp2, hp4, IC=ic, ancestors=hp_ancestors)
hpDef[which(hpDef$id %in% c(hp3, hp4)), 1:2]
calcHpSim(hp3, hp4, IC=ic, ancestors=hp_ancestors)

Example output

Loading required package: BiocParallel
             id         name
401  HP:0000518     Cataract
9645 HP:0030084 Clinodactyly
[1] 0
             id             name
1601 HP:0002119 Ventriculomegaly
9645 HP:0030084     Clinodactyly
[1] 0
             id                      name
1012 HP:0001305 Dandy-Walker malformation
9645 HP:0030084              Clinodactyly
[1] 0.713151
             id                      name
1012 HP:0001305 Dandy-Walker malformation
1601 HP:0002119          Ventriculomegaly
[1] 2.850015

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