doImport: doImport

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

doImport

Description

Performs input for the given DNA methylation and genotyping data.

Usage

doImport(
  data.location,
  s.anno = NULL,
  assembly.meth = "hg19",
  assembly.geno = "hg19",
  tab.sep = ",",
  s.id.col = "sample_id",
  out.folder = tempdir(),
  ...
)

Arguments

data.location	Named character vector specifying the data location. The names correspond to: idat.dir Path to the DNA methylation data. Can be in the form of IDAT files or in any other format accepted by RnBeads geno.dir Path to the genotyping data file directory, either containing PLINK files (i.e. with bed, bim and fam files), imputed, (dosage) files (i.e. with dos and txt files), or idat files
s.anno	Path to the sample annotation sheet. If NULL, the program searches for potential sample annotation sheets in the data location directories.
assembly.meth	Assembly used for the DNA methylation data. Typically is "hg19" for Illumina BeadArray data.
assembly.geno	Assembly used for the genotyping data. If it is not the same as assembly.geno, the positions will be matched using liftOver.
tab.sep	The table separator used for the sample annotation sheet.
s.id.col	The column name of the sample annotation sheet that specifies the sample identifier.
out.folder	The output directory to store diagnostic plots
...	Futher parameters passed to e.g. doGenoImport

Details

Import of DNA methylation and genotyping data is done separately:

DNA methylation data

DNA methylation data is imported using the RnBeads package. We use a default option setting commonly used for DNA methylation data obtained from the Illumina BeadArray series. If you want to specify further options, we refer to the rnb.options.

Genotyping data

Genotyping data is processed using PLINK. We focus on genotyping data generated with the Illumina BeadArray series and use default options. For further option settings, you should consult the qtlSetOption documentation.

You can specify the import type using qtlSetOption through the options meth.data.type and geno.data.type.

This function internally uses doMethImport and doGenoImport

Value

An object of type MethQTLInput-class with the methylation and genotyping information added.

Author(s)

Michael Scherer

Examples

 meth.qtl.in <- loadMethQTLInput(system.file("extdata","reduced_methQTL",package="MAGAR"))
 meth.qtl.in

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