RnBSet-class: RnBSet Class

Description

Basic class for storing DNA methylation and experimental quality information

Arguments

Slots

pheno: Sample annotations (phenotypic and processing data) in the form of a data.frame.
sites: A matrix object storing the identifiers of the methylation sites for which the methylation information is present
meth.sites: matrix of methylation values. Every row corresponds to a methylation site, and every column - to a sample.
covg.sites: matrix of coverage values. Every row corresponds to a methylation site, and every column - to a sample.
regions: list of all identifiers of methylation sites for which methylation information is available.
meth.regions: list of methylation matrix objects, one per available region type. Every row in a matrix corresponds to a methylation site, and every column - to a sample.
covg.regions: list of coverage matrix objects, one per available region type. Every row corresponds to a region, and every column - to a sample.
status: list with meta-information about the object.
assembly: character vector of length one, specifying the genome assembly which the object is linked to, e.g. "hg19".
target: character vector of length one, specifying the feature class: "CpG" for sequencing data, "probes450" and "probes27" for HumanMethylation450 and HumanMethylation27 microarrays respectively.
inferred.covariates: list with covariate information. Can contain elements "sva" and "cell.types".
version: Package version in which the dataset was created.

Methods and Functions

pheno: Gets the phenotypic and processing data of the dataset.
samples: Gets the identifiers of all samples in the dataset.
summarized.regions: Gets the genomic annotations for which methylation data is present.
meth: Gets a matrix of methylation values in the dataset.
mval: Gets a matrix of M values in the dataset.
covg: Gets the matrix of coverage values of the dataset.
remove.sites: Removes sites from the dataset.
remove.samples: Removes samples from the dataset.
addPheno,RnBSet-method: Add sample annotation to the dataset.
combine: Combines two datasets.
regionMapping,RnBSet-method: Retrieve the sites mapping to a given region type
rnb.sample.summary.table: Creates a sample summary table from an RnBSet object.

Details

It is a virtual class and objects of type RnBSet should not be instantiated. Instead, the child classes are used: RnBeadRawSet and RnBeadSet for Infinium HumanMethylation and RnBiseqSet for bisulfite sequencing data