master_pt: Run Monocle, DPT, or PCA-based pseudotime analysis on a...

In maehrlab/thymusatlastools: Tools for analysis of single-cell transcriptomic data

Description

Run Monocle, DPT, or PCA-based pseudotime analysis on a Seurat object.

Usage

master_pt(dge, results_path, method = "monocle", earliest_day = NULL,
  reset_var_genes = T, mp = list(reset_var_genes = reset_var_genes,
  log_scale_expr_thresh = 0.1, excess_disp = 1, num_mature_types = NULL,
  reduction_method = "DDRTree"), ...)

Arguments

dge	Seurat object
results_path	Where to save tables and plots
earliest_day	Numeric. Used to root the Monocle trajectory; gets compared to 'FetchData(dge, "eday")[[1]]' via '=='.
mp	Passed to call_monocle_on_seurat as monocle_params arg.
...	Additional parameters passed to call_monocle_on_seurat. The statistical inference is outsourced to Monocle via call_monocle_on_seurat (or Seurat via pc_as_pt).

maehrlab/thymusatlastools documentation built on May 28, 2019, 2:32 a.m.