get_pca_selected_pcs: Get a final selection of number of PCs.

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

Get a final selection of number of PCs.

Description

The number of PCs and the selection strategy is controlled:

• For single-sample analysis, via PCA_SELECTION_METHOD and PCA_FORCED_PCS parameters in ⁠02_norm_clustering.yaml⁠.

• For integration analysis, via pca_selection_method and pca_forced_pcs subparameters of INTEGRATION_METHODS parameter in ⁠01_integration.yaml⁠.

Usage

get_pca_selected_pcs(
  sce_pca,
  pca_elbow_pcs,
  pca_gene_var_pcs,
  pca_selection_method = c("elbow", "technical_noise", "forced"),
  pca_forced_pcs = NULL
)

Arguments

sce_pca	A SingleCellExperiment object with calculated PCA.
pca_elbow_pcs	A numeric scalar: number of PCs selected by elbow point strategy.
pca_gene_var_pcs	A numeric scalar: number of PCs selected by technical noise strategy.
pca_selection_method	A character scalar: final selection strategy.
pca_forced_pcs	A numeric scalar: constant number of PCs defined in config file.

Value

A modified SingleCellExperiment object:

• The full PCA matrix in "pca_all" slot of reducedDim().

• The subsetted PCA matrix in "pca" slot of reducedDim().

• New items added to metadata(): pca_selection_method, pca_selected_pcs

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.