hp_descendants {PCAN} | R Documentation

## HP descendants (Example data)

### Description

HP terms which are descendants of each HP term (including itself) in the Human Phenotype Ontology (http://www.human-phenotype-ontology.org/). Only descendants of 'Phenotypic abnormality' were taken into account.

### Format

A named list of 10962 character vectors.

### Details

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

### Source

http://compbio.charite.de/hudson/job/hpo/1529/artifact/hp/hp.obo

### 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 1.12.0 Index]