qtlPlotSNPCpGInteraction: qtlPlotSNPCpGInteraction

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

qtlPlotSNPCpGInteraction

Description

Compares the methylation states of a given CpG for the genotype states availabe at the given SNP

Usage

qtlPlotSNPCpGInteraction(
  meth.qtl,
  cpg = NULL,
  snp = NULL,
  out.dir = NULL,
  meth.qtl.res = NULL,
  out.name = NULL
)

Arguments

meth.qtl	An object of type MethQTLInput-class containing the methylation and genotype information for the given CpG and the given SNP
cpg	The CpG identifier as a character (e.g. cg12345678)
snp	The SNP identifier as a character (e.g. rs12345678)
out.dir	If specified, the plot is stored as a pdf in this directory
meth.qtl.res	An optional argument of type MethQTLResult-class containing information on the results. If either cpg or snp are NULL, this function sorts the results by increasing p-value and the uses the best results for plotting.
out.name	Optional name for the resulting plot

Value

An object of type ggplot comparing the CpG methylation states as boxplots across the different genotype states

Author(s)

Michael Scherer

Examples

meth.qtl <- loadMethQTLInput(system.file("extdata","reduced_methQTL",package="MAGAR"))
qtlPlotSNPCpGInteraction(meth.qtl,cpg="cg19565884",snp="rs149871695")

MPIIComputationalEpigenetics/MAGAR documentation built on Nov. 10, 2023, 4:16 p.m.