sce_int_pca_df_fn: Compute PCA for each integration method result...

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 PCA for each integration method result (SingleCellExperiment object).

Description

Compute PCA for each integration method result (SingleCellExperiment object).

Usage

sce_int_pca_df_fn(pca_params_df, BPPARAM = BiocParallel::SerialParam())

Arguments

pca_params_df	(input target) A tibble: derived from sce_int_df and integration_methods_df targets. PCA parameters are defined for each integration method in INTEGRATION_METHODS parameter in ⁠01_integration.yaml⁠ config.
BPPARAM	A BiocParallel::BiocParallelParam object.

Value

A modified pca_params_df tibble with appended SingleCellExperiment object with computed PCA. Output target: sce_int_pca_df

The following items of metadata() of each integrated SingleCellExperiment object are added or modified:

• pca_selection_method, pca_selected_pcs: taken from parameters of the integration method.

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