hpByTrait {PCAN} | R Documentation |
Each trait is associated to one or several HP terms.
A data frame with 55311 rows and 3 columns:
HP terms.
Trait database: always "OMIM" here.
Trait ID: OMI IDs here
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.annotations/1039/artifact/misc/phenotype_annotation.tab
## 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),]