RnBeadRawSet-class: RnBeadRawSet-class

In RnBeads: RnBeads

Description

Main class for storing HumanMethylation micorarray data which includes intensity information

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

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