sce_int_dimred_df_fn: Calculate t-SNE and UMAP 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

Calculate t-SNE and UMAP for each integration method result (SingleCellExperiment object).

Description

Calculate t-SNE and UMAP for each integration method result (SingleCellExperiment object).

Usage

sce_int_dimred_df_fn(dimred_params_df, BPPARAM = BiocParallel::SerialParam())

Arguments

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

Value

A modified dimred_params_df tibble with appended SingleCellExperiment object with computed PCA. Output target: sce_int_dimred_df

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