traitDef: Description of Traits (Example data)
In PCAN: Phenotype Consensus ANalysis (PCAN)

Description Format Details Source Examples

Basic information about traits. Only OMIM diseases associated to at least one gene are taken into account.

A data frame with 3675 rows and 3 columns:

db: Always "OMIM" here.
id: The trait ID (OMIM IDs here).
name: The name of the trait.

These data are used to examplify the different functions of the package. More data are available in the MultiHumanPhenoDB package.

ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2015-05.xml.gz

## 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),]

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