doMethQTLChromosome {MAGAR} | R Documentation

## doMethQTLChromosome

### Description

This functions computes the methQTL interactions for a single chromosome

### Usage

    doMethQTLChromosome(
      meth.qtl,
      chrom,
      sel.covariates = NULL,
      p.val.cutoff = 1e-05,
      out.dir = NULL,
      ncores = 1
    )

### Arguments

`meth.qtl` | An Object of type `MethQTLInput-class`.
`chrom` | Character vector represeting the chromosome to be investigated.
`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 used for methQTL calling
`out.dir` | Optional argument specifying the output directory
`ncores` | The number of cores to be used

### Value

A data frame with seven columns:

CpGs

  The CpG ID chosen to be the representative CpG in the methQTL

SNP

  The SNP ID (as rsNNNNNN) involved in the methQTL

Beta

  The coefficient estimate of the linear model

P.value

  The p-value associated with the coefficient estimate

Chromosome

  The chromosome name

Position.CpG

  The genomic position of the CpG

Position.SNP

  The genomic position of the SNP

Distance

  The distance between the CpG and the SNP

### Author(s)

Michael Scherer

### See Also

doMethQTL

### Examples

    meth.qtl <- loadMethQTLInput(system.file("extdata","reduced_methQTL",package="MAGAR"))
    meth.qtl.res <- doMethQTLChromosome(meth.qtl,chrom="chr18",p.val.cutoff=0.01)

[Package MAGAR version 1.2.0 Index]