sce_compute_dimreds: Compute t-SNE and UMAP dimreds on a 'SingleCellExperiment'...

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Compute t-SNE and UMAP dimreds on a SingleCellExperiment object.

Description

Compute t-SNE and UMAP dimreds on a SingleCellExperiment object.

Usage

sce_compute_dimreds(
  sce_pca_selected_pcs,
  tsne_perp,
  tsne_max_iter,
  dimred = "pca",
  n_dimred = "selected_pcs",
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

sce_pca_selected_pcs	A SingleCellExperiment object with calculated PCA and known number of selected PCs.
tsne_perp	A numeric scalar: t-SNE perplexity.
tsne_max_iter	A numeric scalar: number of t-SNE iterations.
dimred	A character scalar: name of matrix in reducedDim() used to calculate the dimreds.
n_dimred	A character scalar "selected_pcs": if dimred is "pca", then use selected PCs stored in metadata(sce_pca_selected_pcs)$pca_selected_pcs NULL: use all dimensions of dimred An integer scalar: use first n_dimred dimensions of dimred
BPPARAM	A BiocParallel::BiocParallelParam object.

Value

A SingleCellExperiment object with calculated t-SNE and UMAP dimreds. Column names of matrices of these dimreds will be named ⁠tsne_<i>⁠ and ⁠umap_<i>⁠, respectively.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.