hp_descendants: HP descendants (Example data)

In PCAN: Phenotype Consensus ANalysis (PCAN)

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"
)

Example output

Loading required package: BiocParallel

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