getDiffCase: Get the C/T proportion at a selected site, differentially...

In belleau/methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Description

Simulate the proportion of C/T for each case at a selected site, differentially methylated or not.

Usage

getDiffCase(ctrlMean, ctrlVar, selectedAsDM, nbCase, sDiff, nbDiffCase)

Arguments

ctrlMean	a double, the mean of the CTRL at the site.
ctrlVar	a double, the variance of the CTRL at the site.
selectedAsDM	a integer, 1 if the site is selected as differentially methylated, otherwise 0.
nbCase	a integer, the number of cases.
sDiff	a non-negative double included in [0,1], the proportion of C/T for a case differentially methylated that follows a beta distribution where the mean is shifted of vDiff from the CTRL distribution.
nbDiffCase	an integer, the number of cases differentially methylated.

Value

a vector containing 3 + nbCase entries of type double:

• The mean proportion of C/T of the differentially methylated cases

• The number of cases simulated using shifted distribution

• The number of cases simulated using the control distribution

• The proportion of C/T for each case

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## Fix seed to obtain replicable results
set.seed(2010)

## Get the proportion of C/T for each case at a specific site.
methInheritSim:::getDiffCase(ctrlMean = 0.9814562, ctrlVar = 
0.0003607153, selectedAsDM = 0, nbCase=6, sDiff = 0.8, 
nbDiffCase = round(6 * 0.9))

belleau/methInheritSim documentation built on April 1, 2020, 2:43 p.m.