doImport {MAGAR} | R Documentation

## 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

[Package MAGAR version 1.0.1 Index]