hpDef {PCAN} | R Documentation |
HP terms basic information. Only descendants of 'Phenotypic abnormality' were taken into account.
A data frame with 10962 rows and 2 columns:
HP term IDs
HP term names
These data are used to examplify the different functions of the package. More data are available in the MultiHumanPhenoDB package.
http://compbio.charite.de/hudson/job/hpo/1529/artifact/hp/hp.obo
## 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)