computeHpIC: Compute Information Content (IC) for each HP based on genes...

In PCAN: Phenotype Consensus ANalysis (PCAN)

Description

Compute Information Content (IC) for each HP based on genes by HP

Usage

computeHpIC(content, hp.descendants)

Arguments

content	a list providing the content associated to each HP
hp.descendants	a list providing for each HP all its descendant HP terms

Details

This function assumes that all the HP terms taken into account belong to the same family of terms(i.e they are all descendants of the same term).

Value

a vector of IC named with HP terms

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.