Extract matrix of embeddings — Embeddings.liger (original) (raw)

Extract matrix containing iNMF or dimensionality reduction embeddings.

# S3 method for liger
Embeddings(object, reduction = NULL, iNMF = FALSE, check_only = FALSE, ...)

Arguments

object

LIGER object name.

reduction

name of dimensionality reduction to pull

iNMF

logical, whether to extract iNMF h.norm matrix instead of dimensionality reduction embeddings.

check_only

logical, return TRUE if valid reduction is present.

...

Arguments passed to other methods

Examples

if (FALSE) {
# Extract embedding matrix for current dimensionality reduction
UMAP_coord <- Embeddings(object = liger_object)

# Extract iNMF h.norm matrix
iNMF_mat <- Embeddings(object = liger_object, reduction = "iNMF")
}