RnBSet-class: RnBSet Class

Description Details Slots Methods and Functions Author(s)

Description

Basic class for storing DNA methylation and experimental quality information

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

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.

imputed

Flag indicating if methylation matrix has been imputed.

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.

isImputed,RnBSet-method

Getter for the imputation slot.

Author(s)

Pavlo Lutsik


RnBeads documentation built on March 3, 2021, 2 a.m.