getSim: Simulate the proportion of C/T at each site of synthetic CHR...

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

Description

For each control and case, generate the proportion of C/T at each of the synthetic CHR.

Usage

getSim(nbCtrl, nbCase, generation, stateInfo, stateDiff, stateInherite,
  diffValue, propDiff, propDiffsd, propInheritance, propHetero)

Arguments

nbCtrl	a positive integer, the number of controls.
nbCase	a positive integer, the number of cases.
generation	a positive integer, the number of generations.
stateInfo	a GRanges object, the synthetic chromosome generated by getSyntheticChr function.
stateDiff	a vector of integer (0 and 1) with length corresponding the length of stateInfo. The vector indicates, using a 1, the positions where the CpG sites are differentially methylated.
stateInherite	a vector of integer (0 and 1) with length corresponding the length of stateInfo. The vector indicates, using a 1, the positions where the CpG values are inherited.
diffValue	a non-negative double between between [0,1], the proportion of C/T for a case differentially methylated following a beta distribution where the mean is shifted of diffValue from the CTRL distribution.
propDiff	a double superior to 0 and inferior or equal to 1, the mean value for the proportion of samples that will have, for a specific position, differentially methylated values. It can be interpreted as the penetrance.
propDiffsd	a non-negative double, the standard deviation associated to the propDiff.
propInheritance	a non-negative double between [0,1], the proportion of case that inherite differentially methylated sites.
propHetero	a non-negative double between [0,1], the reduction of vDiff for the second and following generations.

Value

a GRangesList, the object contains information about the simulation. The file have four metadata related to the real dataset:

• meanDiff, the means of the shifted distribution.

• meanCTRL, the means of the control distribution.

• partitionCase, the number of cases simulated using the shifted distribution.

• partitionCtrl, the number of cases simulated using the control distribution and a metadata for each cases and controls the proportion of C/T.

Author(s)

Pascal Belleau, Astrid Deschenes

Examples

## Fix seed to have reproducible results
set.seed(312)

## Load dataset
data("samplesForChrSynthetic")

## Generate a stateInfo object using samples
stateInformation <- methInheritSim:::getSyntheticChr(methInfo = 
    samplesForChrSynthetic, nbBlock = 1, nbCpG = 3)

## Generate a stateDiff and stateInherite objects with length corresponding 
## to nbBlock * nbCpG from stateInformation
stateDiff  <- c(1, 0, 1)
stateInherite <- c(1, 0, 0)

## Create a simulation using stateInformation, stateDiff and stateInherite
methInheritSim:::getSim(nbCtrl = 3, nbCase = 2, generation = 3, 
    stateInfo = stateInformation, stateDiff = stateDiff, 
    stateInherite = stateInherite, diffValue = 10, 
    propDiff = 0.8, propDiffsd = 0.2, propInheritance = 0.8, 
    propHetero = 0.1)

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