byExtremality: choose loci or features by extremality (fraction of Bernoulli...

In ttriche/biscuitEater: a bunch of convenience functions for Biscuit

Description

For DNA methylation, particularly summarized across regions, we can do better (a lot better) than MAD. Since we know that

Usage

byExtremality(x, r = NULL, k = 500)

Arguments

x	a bsseq object
r	regions to consider (default is NULL, all loci... !)
k	how many rows/regions to return (500)

Details

max(SD(X_j)) if X_j ~ Beta(a, b) < max(SD(X_j)) if X_j ~ Bernoulli(a/(a+b))

for X having a known mean and SD, hence solvable for a + b by MoM, define

extremality = sd(X_j) / bernoulliSD(mean(X_j))

This function finds the k most extremal features in x & returns their values. For count-based proportions,

Value

a matrix-like object with methylation values, by extremality

ttriche/biscuitEater documentation built on May 15, 2019, 4:18 p.m.