RnBeadRawSet-class: 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

Matrix of intensities for the probes measuring the abundance of methylated molecules

Matrix of intensities for the probes measuring the abundance of unmethylated molecules

Matrix of "out-of-band" intensities for the probes measuring the abundance of methylated molecules

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.

...

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.