geneDef {PCAN}R Documentation

Description of genes (Example data)

Description

Basic information about genes Only genes associated to at least one OMIM disease are taken into account.

Format

A data frame with 3265 rows and 3 columns:

entrez

Entrez gene ID.

name

Gene name.

symbol

Gene symbol.

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),]

[Package PCAN version 1.21.0 Index]