doMethQTLChromosome: doMethQTLChromosome

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

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)

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