geneDef: Description of genes (Example data)

In PCAN: Phenotype Consensus ANalysis (PCAN)

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),]

Example output

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

PCAN documentation built on Nov. 8, 2020, 6:47 p.m.