geneByHp: Entrez gene IDs associated to HP terms (Example data)

In PCAN: Phenotype Consensus ANalysis (PCAN)

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"
)

Example output

Loading required package: BiocParallel

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