Description Usage Arguments Value Author(s)

View source: R/batch.quality.R

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

1 | ```
rnb.execute.batch.qc(rnb.set, pcoordinates, permutations = NULL)
``` |

`rnb.set` |
HumanMethylation450K dataset as an object of type |

`pcoordinates` |
Coordinates of the samples of |

`permutations` |
Matrix of sample index permutations, as returned by |

`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`

.

Pavlo Lutsik

RnBeads documentation built on March 18, 2018, 2:37 p.m.

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