simDMRs {dmrseq} | R Documentation

## Simulate Differentially Methylated Regions

### Description

Add simulated DMRs to observed control data. Control data will be split into two (artificial) populations.

### Usage

    simDMRs(bs, num.dmrs = 3000, delta.max0 = 0.3)

### Arguments

`bs` | a BSseq object containing only control samples (from the same population) for which simulated DMRs will be added after dividing the population into two artificial groups.
`num.dmrs` | an integer specifying how many DMRs to add.
`delta.max0` | a proportion value indicating the mode value for the difference in proportion of methylated CpGs in the simulated DMRs (the actual value will be drawn from a scaled Beta distribution centered at this value). Default value is 0.3.

### Value

A named list object with 5 elements: (1) `gr.dmrs` is a `GenomicRanges` object with `num.dmrs` ranges that represent the random DMRs added. (2) `dmr.mncov` is a numeric vector that contains the mean coverage in each simulated DMR. (3) `dmr.L` is a numeric vector that contains the number of CpGs in each simulated DMR. (4) `bs` is the BSseq object that contains the simulated DMRs. (5) `deltas` is a numeric vector that contains the effect size used for each DMR.

### Examples

    # Add simulated DMRs to a BSseq dataset
    # This is just for illustrative purposes - ideally you would
    # add DMRs to a set of samples from the same condition (in our
    # example data, we have data from two different cell types)
    # In this case, we shuffle the samples by cell type to create
    # a null comparison.

    data(BS.chr21)

    BS.chr21.sim <- simDMRs(bs=BS.chr21[1:10000,c(1,3,2,4)],
                            num.dmrs=50)

    # show the simulated DMRs GRanges object
    show(BS.chr21.sim$gr.dmrs)

    # show the updated BSseq object that includes the simulated DMRs
    show(BS.chr21.sim$bs)

    # examine effect sizes of the DMRs
    head(BS.chr21.sim$delta)

[Package dmrseq version 1.8.0 Index]