MethQTLInput-class {MAGAR} | R Documentation

## MethQTLInput-class

### Description

Class storing methQTL input data, such as DNA methylation and genotyping data, as well as sample metadata

### Details

This class is the basis for computing methQTLs in the methQTL-package. It stores all the relevant information including methylation data and genotype data as a matrix or HDF5Matrix, the phenotypic data as a data frame and the genomic annotation of both the methylation sites and the SNP data.

### Slots

`meth.data`

  The methylation data as a numeric matrix of beta values or as an object of type `HDF5Matrix`

`geno.data`

  The genotyping data as a numeric matrix of SNP genotypes (0=homozygote reference, 1=heterozygote, 2=homozygote alternative allele) or as an object of type `HDF5Matrix`

`pheno.data`

  Phenotypic data describing the samples used in the study. Matches the dimensions of both `meth.data` and `geno.data`

`anno.meth`

  Genomic annotation of the methylation sites as a `data.frame`. Has the same number of rows as `meth.data`.

`anno.geno`

  Genomic annotation of the SNPs as a `data.frame`. Has the same number of rows as `geno.data`.

`samples`

  The sample identifiers used both for `meth.data` and `geno.data`, and as the rownames of `pheno.data`.

`assembly`

  The genome assembly used.

`platform`

  The platform used to compute the methylation data.

`disk.dump`

  Flag indicating if the matrices are stored on disk rather than in memory.

`imputed`

  Flag indicating if genotype dataset has been imputed.

### Methods

`getMeth`

  Returns the methylation matrix.

`getGeno`

  Returns the genotyping matrix.

`getPheno`

  Returns the phenotypic information.

`getAnno`

  Returns the genomic annotation.

`saveMethQTLInput`

  Stores the object on disk.

`imputeMeth`

  Imputes the DNA methylation data matrix

### Author(s)

Michael Scherer

[Package MAGAR version 1.2.0 Index]