estimateRho: Helper function for estimating the dispersion factor rho

In gerstung-lab/deepSNV: Detection of subclonal SNVs in deep sequencing data.

Helper function for estimating the dispersion factor rho

Description

It uses a method of moments approximation to estimate rho from the variances of the relative frequencies nu across samples

Usage

estimateRho(x, mu, ix, pseudo.rho = .Machine$double.eps)

Arguments

x	counts
mu	relative frequency across all samples
ix	index indicating the set of samples to use (typically indicating those with relative frequency smaller than 0.1).
pseudo.rho	a pseudo count added to each sample to avoid problems with zeros. Default = .Machine$double.eps

Value

rho

Note

Experimental code, subject to changes

Author(s)

mg14

gerstung-lab/deepSNV documentation built on June 3, 2022, 3:05 p.m.