MethQTLInput-class: MethQTLInput-class

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

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

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