geneByTrait: Gene associated to trait (Example data)

In PCAN: Phenotype Consensus ANalysis (PCAN)

Description

Each trait is associated to one or several genes. Only genes associated to OMIM disease with a "Pathogenic" clinical status and one of the follwing origins: "germline", "de novo", "inherited", "maternal", "paternal", "biparental", "uniparental".

Format

A data frame with 4569 rows and 3 columns:

entrez

Entrez gene IDs.

db

Trait database: always "OMIM" here.

id

Trait ID: OMI IDs here

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

data(geneByTrait, traitDef, geneDef, package="PCAN")
omim <- "612285"
traitDef[which(traitDef$id==omim),]
# Gene associated to this disease
entrez <- geneByTrait[which(geneByTrait$id==omim), "entrez"]
geneDef[which(geneDef$entrez %in% entrez),]
# All diseases associated to this gene
traitDef[
     which(
         traitDef$id %in%
         geneByTrait[which(geneByTrait$entrez==entrez), "id"]
     ),
]

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