PCA results container

Stores a PCA fit (from stats::prcomp()) computed over methylation windows.

mesaPCA(prcomp, windows)

# S4 method for class 'mesaPCA'
show(object)

Arguments

prcomp: prcomp PCA fit from stats::prcomp(). Default: none.
windows: character() Window IDs used. Default: none.
object: mesaPCA

Value

A mesaPCA object containing the PCA fit and window IDs.

Details

A valid object has non-empty windows with no NA or duplicates, one per row of prcomp$rotation, and a prcomp$x matrix whose row names are the sample IDs.

Slots

prcomp: prcomp A PCA fit returned by stats::prcomp().
windows: character() Window IDs used in the PCA.

Accessors

getPrcomp(): the prcomp fit, e.g. for sdev or rotation;
getCoordinates(): the sample coordinates (prcomp$x), as a data.frame;
getSampleNames(): the sample IDs (row names of prcomp$x);
getWindowNames(): the window IDs (windows).

Examples

set.seed(1)
x <- matrix(rnorm(20), nrow = 5, ncol = 4,
    dimnames = list(paste0("S", 1:5), paste0("W", 1:4)))
pc <- stats::prcomp(x, center = TRUE, scale. = FALSE)
mp <- mesaPCA(prcomp = pc, windows = colnames(x))
mp
#> PCA result for 5 samples calculated over 4 windows