Description Usage Arguments Value Author(s) See Also Examples

Performs tests for association between traits and principal components.

1 | ```
rnb.execute.batcheffects(rnb.set, pcoordinates = NULL)
``` |

`rnb.set` |
Methylation dataset as an object of type inheriting |

`pcoordinates` |
Coordinates of the samples of |

Results of attempted tests for associations in the form of a list with up to three elements:

`"permutations"`

`integer`

matrix of index permutations. The number of rows in the matrix is*N*- the number of samples in`rnb.set`

. Every column in this matrix denotes a sample permutation; the first column is the sequence 1 to*N*. This element is included only when`rnb.getOption("exploratory.correlation.permutations")`

is non-zero and there are numeric traits to be tested.`"pc"`

List of four matrices named

`"failures"`

,`"tests"`

,`"correlations"`

and`"pvalues"`

. The rows in each of these matrices correspond to the first several principal components, and the columns - to selected traits. This element is not included in the returned list when`pcoordinates`

is`NULL`

.`"traits"`

List of four square symmetric matrices named

`"failures"`

,`"tests"`

,`"correlations"`

and`"pvalues"`

, containing information about the performed tests for pairwise trait association. This element is included only if two or more traits were tested.

Yassen Assenov

`rnb.run.exploratory`

for running the whole exploratory analysis module

1 2 3 4 5 6 7 | ```
library(RnBeads.hg19)
data(small.example.object)
regs <- c("sites", summarized.regions(rnb.set.example))
dreduction <- function(x) rnb.execute.dreduction(rnb.set.example, x)
pcoordinates <- lapply(regs, dreduction)
names(pcoordinates) <- regs
result <- rnb.execute.batcheffects(rnb.set.example, pcoordinates)
``` |

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