Performs tests for association between traits and principal components.
Methylation dataset as an object of type inheriting
Coordinates of the samples of
Results of attempted tests for associations in the form of a list with up to three elements:
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.
List of four matrices named
"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
List of four square symmetric matrices named
"pvalues", containing information about the performed tests for
pairwise trait association. This element is included only if two or more traits were tested.
rnb.run.exploratory for running the whole exploratory analysis module
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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)