getLogitFracMeth: helper function for compartment inference...

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

Description

We want something with nominally Gaussian error for compartment inference, so this function grabs suitable (default >= 3 reads in >=2 sample) measurements and turns them into lightly moderated, logit-transformed methylated-fraction estimates (also known, unfortunately, as M-values) for compartment calling, by performing Dirichlet smoothing (adding k reads to M and U support).

Usage

getLogitFracMeth(x, minCov = 3, minSamp = 2, k = 0.1, r = NULL)

Arguments

x	a BSseq object with methylated and total reads
minCov	minimum read coverage for landmarking samples (3)
minSamp	minimum landmark samples with >= minCov (2)
k	pseudoreads for smoothing (0.1)
r	regions to collapse over (default is NULL, do it by CpG)

Value

       smoothed logit(M/Cov) matrix with coordinates as row names

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