calcRP: low level Rank Product function

Description Usage Arguments Details Value Note References See Also

View source: R/rankProduct.R

Description

Calculates the Rank Product from a set of gene rank probabilities

Usage

1
calcRP(x)

Arguments

x

numeric vector of gene rank probabilities

Details

The low level calculation of the RP value, as described in the Rank Product paper by Rainer Breitling. Given an ordering of N genes in a differential expression result, the probability of a gene occuring at position j is given by (j/N). With a set of K replicates, Breitling defines the RP value for a gene as the K'th root of the product of the probabilities from all K replicates.

Value

numeric value of length 1, equivalent to the geometric mean of x

Note

Implemented via log2(x) for numerical stability, and further normalized by the number of replicates K to allow comparisons between datasets.

As implemented, it is equivalent to logmean. Contrast with mean and sqrtmean.

References

Breitling, R. FEBS Letters 573 (2004)

See Also

rankProduct, rankProductDiffExpress, for the higher level routines based on Rank Product


robertdouglasmorrison/DuffyTools documentation built on Dec. 7, 2018, 8:02 a.m.