geneByHp {PCAN} | R Documentation

## Entrez gene IDs associated to HP terms (Example data)

### Description

Each entrez gene IDs is associated to one or several HP terms

### Format

A data frame with 67989 rows and 2 columns:

entrez

  entrez gene IDs

hp

  HP terms

### Details

These data are used to examplify the different functions of the package. More data are available in the MultiHumanPhenoDB package.

### Source

Two ressources were used in May 27 2015:

- ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_2015-05.xml.gz was used to find genes associated to each OMIM disease with a "Pathogenic" clinical status and one of the follwing origins: "germline", "de novo", "inherited", "maternal", "paternal", "biparental", "uniparental".

- http://compbio.charite.de/hudson/job/hpo.annotations/1039/artifact/misc/phenotype_annotation.tab was used to find HP associated to each OMIM disease.

### Examples

    ###########################################
    ## Compute information content of each HP according to associated genes
    data(geneByHp, hp_descendants, package="PCAN")
    geneByHp <- unstack(geneByHp, entrez~hp)
    ic <- computeHpIC(geneByHp, hp_descendants)
    hist(
        ic,
        breaks=100, col="grey",
        main="Distribution of Information Content",
        xlab="IC base on genes associated to HP"
    )

[Package PCAN version 1.17.0 Index]