RnBeadRawSet-class {RnBeads} | R Documentation |
Main class for storing HumanMethylation micorarray data which includes intensity information
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 )
pheno |
Phenotypic data. |
probes |
|
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 |
|
beta.offset |
A regularization constant which is added to the denominator at beta-value calculation |
summarize.bead.counts |
If |
summarize.regions |
... |
region.types |
A |
useff |
If |
ffcleanup |
If |
an object of class RnBeadRawSet
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.
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.
Pavlo Lutsik