scandal_setup_analysis: Setup analysis tools

In dravishays/scandal: A framework for single-cell analysis

Description

This function sets-up analysis-related tools such as computing a cell-correlation matrix, t-SNE and UMAP to be used later in downstream analysis.

Usage

scandal_setup_analysis(
  object,
  computation_opts = c(correlation = TRUE, tsne = TRUE, umap = TRUE),
  cor_method = "pearson",
  tsne_perplexity = 30,
  tsne_pca = TRUE,
  tsne_initial_dims = 50,
  tsne_pca_center = TRUE,
  tsne_pca_scale = FALSE,
  tsne_normalize = TRUE,
  umap_config = scandal_default_umap_config(),
  verbose = FALSE
)

Arguments

umap_config

Author(s)

Avishay Spitzer

dravishays/scandal documentation built on Jan. 8, 2020, 1:30 p.m.