doMethQTL: doMethQTL

In MPIIComputationalEpigenetics/MAGAR: MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

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)

MPIIComputationalEpigenetics/MAGAR documentation built on Dec. 6, 2024, 2:30 p.m.