rnb.execute.batch.qc {RnBeads} | R Documentation

## 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`.

### Author(s)

Pavlo Lutsik

[Package RnBeads version 2.2.0 Index]