Description of Traits (Example data)

Description

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

Format

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.

Details

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

Source

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

Examples

## 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),]