RnBeadSet-class: RnBeadSet Class
In RnBeads: RnBeads

Description Usage Arguments Details Value Slots Methods and Functions Author(s)

Stores the preprocessed information from HumanMethylation experiments

RnBeadSet(
  pheno,
  probes,
  betas,
  p.values = NULL,
  bead.counts = NULL,
  qc = NULL,
  platform = "450k",
  summarize.regions = TRUE,
  region.types = rnb.region.types.for.analysis("hg19"),
  useff = rnb.getOption("disk.dump.big.matrices")
)

`pheno`	Phenotypic data.
`probes`	`character` vector of Infinium(R) probe identifiers
`betas`	`matrix` or `ff_matrix` of beta values. If `probes` are missing should contain Infinium probe identifiers as row names.
`p.values`	`matrix` or `ff_matrix` of detection p-values.
`bead.counts`	...
`qc`	...
`platform`	`character` singleton specifying the microarray platform: `"450k"` corresponds to HumanMethylation450 microarray, and `"27k"` stands for HumanMethylation27.
`summarize.regions`	...
`region.types`	A `character` vector specifying the region types, for which the methylation infromation will be summarized.
`useff`	If `TRUE` the data matrices will be stored as `ff` objects

There are multiple ways to create an object of type RnBeadSet:

Loading from files: Dataset can be loaded from text or binary files. See the function rnb.execute.import for more details.
Downloading from GEO: See the function rnb.read.geo for details.
Converting from MethyLumiSet: ...

an object of class RnBeadSet

pval.sites: matrix of detection p-values with the same dimensions as betas, or NULL if the detection p-values are not available.
pval.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.sites: matrix of bead counts per probe with the same dimensions as betas, or NULL if this data are not available.
qc: Quality control probe information in the form of a list of two elements - "Cy3" and "Cy5", storing intensities of probes on the green and red channels, respectively. This slot's value is NULL if no control probe information is available.

samples: Gets the identifiers of all samples in the dataset.
pheno: Gets the phenotypic and processing data of the dataset.
meth: Gets the matrix of methylation beta-values of the dataset.
dpval: Gets the matrix of detection p-values of the dataset.
covg: Gets the matrix of bead counts of the dataset.
qc: Gets the intensities of the quality control probes.
remove.sites: Removes probes from the dataset.
remove.samples: Removes samples from the dataset.
combine: Combines two datasets.