geneByTrait {PCAN} | R Documentation

## Gene associated to trait (Example data)

### 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"]
         ),
    ]

[Package PCAN version 1.20.0 Index]