doMethQTL {MAGAR} | R Documentation

## doMethQTL

### Description

Function to compute methQTL given DNA methylation and genotyping data.

### Usage

    doMethQTL(
      meth.qtl,
      sel.covariates = NULL,
      p.val.cutoff = 1e-05,
      ncores = 1,
      cluster.submit = FALSE,
      out.dir = getwd(),
      default.options = TRUE
    )

### Arguments

`meth.qtl` | An object of type `MethQTLInput-class` on which methQTL computation is to be performed
`sel.covariates` | Covariates as column names of the sample annotation sheet stored in `meth.qtl` to be used for covariate adjustment.
`p.val.cutoff` | The p-value cutoff used for methQTL calling
`ncores` | The number of cores used.
`cluster.submit` | Flag indicating if jobs are to be distributed among a SGE compute cluster
`out.dir` | Output directory
`default.options` | Flag indicating if default options for `cluster.cor.threshold`, `standard.deviation.gauss`, and `absolute.distance.cutoff` should be loaded for the data set used. See the option settings in `'inst/extdata'`.

### Details

The process is split into 4 steps:

1

  First the two matrices are split according to the chromosomes.

2

  We then compute correlations among the CpGs and compute CpG correlation blocks.

3

  In each of the CpG correlation blocks, linear models according to the `linear.model.type` `qtlSetOption` with the CpG methylation state of the reference CpG specified by `representative.cpg.computation` as output and the SNP genotype state and all possible covariates as input are computed.

4

  For each of the CpG correlation blocks, we report the p-value of the representative CpG.

Currently, if `qtlGetOption('cluster.architecture')=='sge'` the function does not return a `MethQTLResult` object, but `NULL`, since monitoring finished jobs is hard through SLURM. After the jobs are finished (checked using `squeue`), the results can can be loaded from `out.dir` using `loadMethQTLResult`.

### Value

An object of type `MethQTLResult-class` containing the called methQTL interactions.

### Author(s)

Michael Scherer

### See Also

doMethQTLChromosome

### Examples

    meth.qtl <- loadMethQTLInput(system.file("extdata","reduced_methQTL",package="MAGAR"))
    meth.qtl.res <- doMethQTL(meth.qtl,p.val.cutoff=0.01)

[Package MAGAR version 1.2.0 Index]