RnBeads (version 1.4.0)

rnb.execute.batcheffects: rnb.execute.batcheffects

Description

Performs tests for association between traits and principal components.

Usage

rnb.execute.batcheffects(rnb.set, pcoordinates = NULL)

Arguments

rnb.set

Methylation dataset as an object of type inheriting RnBSet.

pcoordinates

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

Value

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.

See Also

rnb.run.exploratory for running the whole exploratory analysis module

Examples

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)