Embeddings: Extract matrix of embeddings

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Extract matrix of embeddings

Description

Extract matrix containing iNMF or dimensionality reduction embeddings.

Usage

## S3 method for class '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

Value

matrix

Examples

## Not run: 
# 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")

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.