getAssocTestRes.pca: getAssocTestRes.pca
In demuellae/muRtools: Mueller's R tools

getAssocTestRes.pca

R Documentation

getAssocTestRes.pca

Description

Test associations of annotations with principal components (PCA)

Usage

getAssocTestRes.pca(X, ph, nComp = 10, nPerm = 1000)

Arguments

`X`	A matrix on which the dimension reduction is to be performed. Alternatively, it can be a matrix of PC coordinates computed by `getDimRedCoords.pca`.
`ph`	annotation table for the datapoints. The columns of this table will be used to test associations with the PCs. Should be a `matrix` or `data.frame`.
`nComp`	number of PCs to be considered
`nPerm`	number of permutation tests to be conducted if an annotation in `ph` is numeric (i.e. a correlation permutation test is performed)

Value

A nested list of tested associations one element for each column in ph (1st level), each PC (2nd level). Each element is again a list with the name of the test being used (test), the test statistic (statistic) and p-value (pvalue)