R: RnBeadRawSet-class

RnBeadRawSet-class {RnBeads}

R Documentation

RnBeadRawSet-class

Description

Main class for storing HumanMethylation micorarray data which includes intensity information

Wrapper function RnBeadRawSet

Usage

RnBeadRawSet(pheno, probes, M, U, M0 = NULL, U0 = NULL,
  bead.counts.M = NULL, bead.counts.U = NULL, p.values = NULL,
  qc = NULL, platform = "450k", beta.offset = 100,
  summarize.bead.counts = TRUE, summarize.regions = TRUE,
  region.types = rnb.region.types.for.analysis("hg19"),
  useff = rnb.getOption("disk.dump.big.matrices"), ffcleanup = FALSE)

Arguments

`pheno`	Phenotypic data.
`probes`	`character` vector of Infinium(R) probe identifiers
`M`	Matrix of intensities for the probes measuring the abundance of methylated molecules
`U`	Matrix of intensities for the probes measuring the abundance of unmethylated molecules
`M0`	Matrix of "out-of-band" intensities for the probes measuring the abundance of methylated molecules
`U0`	Matrix of "out-of-band" intensities for the probes measuring the abundance of unmethylated molecules
`bead.counts.M`	Matrix of bead counts per probe.
`bead.counts.U`	Matrix of bead counts per probe.
`p.values`	Matrix of detection p-values.
`qc`	...
`platform`	`character` singleton specifying the microarray platform: `"450k"` corresponds to HumanMethylation450 microarray, and `"27k"` stands for HumanMethylation27.
`beta.offset`	A regularization constant which is added to the denominator at beta-value calculation
`summarize.bead.counts`	If `TRUE` the coverage slot is filled by summarizing the `bead.counts.M` and `bead.counts.U` matrices. For type I probes the summarization is done using `min` operation, while for type II probes the bead counts should be identical in both supplied matrices
`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
`ffcleanup`	If `TRUE` and disk dumping has been enabled the data of the input `ff` objects will be deleted

Value

an object of class RnBeadRawSet

Slots

pheno: Phenotypic data.
M: matrix of intensities for the probes measuring the abundance of methylated molecules.
U: matrix of intensities for the probes measuring the abundance of unmethylated molecules.
M0: matrix of "out-of-band" intensities for the probes measuring the abundance of methylated molecules.
U0: matrix of "out-of-band" intensities for the probes measuring the abundance of unmethylated molecules.
bead.counts.M: matrix of bead counts per probe.
bead.counts.U: matrix of bead counts per probe.

Methods and Functions

samples: Gets the identifiers of all samples in the dataset.
M: Get the matrix of intensities for the probes measuring the abundance of methylated molecules.
U: Get the matrix of intensities for the probes measuring the abundance of unmethylated molecules.
intensities.by.color: Get probe intensities in each color channel.

Author(s)

Pavlo Lutsik

[Package RnBeads version 1.10.8 Index]