geneByTrait {PCAN} | R Documentation |
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".
A data frame with 4569 rows and 3 columns:
Entrez gene IDs.
Trait database: always "OMIM" here.
Trait ID: OMI IDs here
These data are used to examplify the different functions of the package. More data are available in the MultiHumanPhenoDB package.
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2015-05.xml.gz
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"] ), ]