ExploreIteratively: Explore a single-cell dataset, alternating between gene...

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

Description

Explore a single-cell dataset, alternating between gene selection and clustering.

Usage

ExploreIteratively(dge, log_fc = 0.25, eligible_genes = NULL, maxiter = 5,
  tol = 10, verbose = T, cluster_method = function(...)
  Seurat::FindClusters(..., print.output = F), num_pc = 25, ...)

Arguments

dge	Seurat object.
log_fc	Passed to RefineVariableGenes.
eligible_genes	Restricts the set of genes used. Try setting it to 'get_mouse_tfs()'.
maxiter	Iteration limit. Issues warning if hit.
tol	If the list changes by less than this many genes (added + removed), it stops.
cluster_method	A user-provided function to re-estimate clusters, modeled off Seurat::FindClusters. It should take a Seurat object as the first arg. It should also accept a 'pc.use' input (even if you just discard it). For your convenience, the principal components get updated before this function is called. The TSNE embedding doesn't, so don't use DBClustDimension alone.
num_pc	Used in recomputing the number of PCs, and '1:num_pc' is passed to 'cluster_method' as 'pc.use'.
...	Extra parameters passed to 'cluster_method'

Value

List with names "dge" (the updated seurat object) and "iteration_stats" (numbers of genes present, added, and removed at each iteration.)

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