R/runMNN.R

In erikjskie/ensemblemerge: Integrates existing sc-RNAseq integration methods into a single package

#' Run fastMNN merging
#'
#' @param params a FastMNNParams object
#' @param data a Seurat object
#'
#' @importFrom Seurat VariableFeatures SplitObject RunPCA as.SingleCellExperiment CreateDimReducObject
#' @importFrom SingleCellExperiment reducedDim
#'
#' @return returns a Seurat object with integrated data
#'
run_fastMNN <- function(params, data){

	if (is.null(data@reductions[[params@pca_name]])){
  	data <- RunPCA(
			object = data, 
			npcs = params@npcs, 
			reduction.name = params@pca_name,
			verbose = FALSE
		)
	}
	
	features <- VariableFeatures(data)
	object.list <- SplitObject(data, split.by = params@batch)
	object.list <- lapply(object.list, as.SingleCellExperiment)
	object.list <- lapply(object.list, function(obj) obj[features, ])
	out <- do.call(what = batchelor::fastMNN, args = c(object.list, list(d = params@npcs, k = params@n_neighbors)))

	out <- out[, colnames(data)]

	data[[params@name]] <- CreateDimReducObject(
		embeddings = reducedDim(out, 'corrected'),
		key = params@reduction_key,
		assay = DefaultAssay(data)
	)
	data

}