calcHpSim {PCAN} | R Documentation |
This function compares 2 HP terms based on provided Information Content and ancestors
calcHpSim(term1, term2, method = c("Resnik"), IC, ancestors)
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 |
A numeric value
Patrice Godard
## 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)