getSim: Simulate the proportion of C/T at each site of synthetic CHR...
In methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Description Usage Arguments Value Author(s) Examples

View source: R/methylInheritanceSimInternalMethods.R

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

1 2	getSim(nbCtrl, nbCase, generation, stateInfo, stateDiff, stateInherite, diffValue, propDiff, propDiffsd, propInheritance, propHetero)

`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.

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.

Pascal Belleau, Astrid Deschenes

## 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)