RnBeads (version 1.4.0)

rnb.execute.batch.qc: rnb.execute.batch.qc

Description

Computation of correlations and permutation-based p-values for detecting quality-associated batch effects.

Usage

rnb.execute.batch.qc(rnb.set, pcoordinates, permutations = NULL)

Arguments

rnb.set

HumanMethylation450K dataset as an object of type RnBeadSet.

pcoordinates

Coordinates of the samples of rnb.set in the principal components space, as returned by rnb.execute.dreduction.

permutations

Matrix of sample index permutations, as returned by rnb.execute.batcheffects. If this parameter is NULL, permutation-based p-values are not calculated.

Value

NULL if no principal components for batch analysis are specified ( rnb.getOption("exploratory.principal.components") == 0); otherwise, a hierarchical structure of matrices in the form of a nested list. The root branches are represented by the elements "correlations" and "pvalues". Every element is a list of control probe types; each type is in turn a list of up to two matrices of correlations between probe values and principal components - one for the probes on the green channel and one for the red channel. Note that the "pvalues" branch is not returned when permutations is NULL.