RnBSet-class {RnBeads} | R Documentation

## RnBSet Class

### 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

[Package RnBeads version 2.12.2 Index]