UMAP results container

Stores per-sample coordinates from a UMAP embedding computed over methylation windows.

mesaUMAP(points, windows)

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

Arguments

points

data.frame One row per sample with positions in UMAP space (row names = sample IDs). Default: none.

windows

character() Window IDs used. Default: none.

object

mesaUMAP

Value

A mesaUMAP object containing UMAP coordinates and window IDs.

Details

A valid object has non-empty windows with no NA or duplicates, and at least one row of numeric points with the sample IDs as row names.

Slots

points

data.frame One row per sample with UMAP coordinates (e.g., UMAP1, UMAP2). Row names are sample IDs.

windows

character() Window IDs used to compute the embedding.

Accessors

• getCoordinates(): the sample coordinates (points);

• getSampleNames(): the sample IDs (row names of points);

• getWindowNames(): the window IDs (windows).

See also

mesaDimRed, dimRedAccessors

Examples

pts <- data.frame(UMAP1 = c(0.1, -0.2, 0.0),
    UMAP2 = c(0.3, 0.1, -0.1))
rownames(pts) <- paste0("S", 1:3)
mu <- mesaUMAP(points = pts, windows = c("w1", "w2", "w3"))
mu
#> UMAP result for 3 samples calculated over 3 windows