refine_cl: Refine clusters

In AllenInstitute/scrattch.hicat: Hierarchical Iterative Clustering Analysis for Transcriptomic data

Refine clusters

Description

Refine clusters

Usage

refine_cl(
  cl,
  co.ratio = NULL,
  cl.mat = NULL,
  confusion.th = 0.6,
  min.cells = 4,
  niter = 50,
  tol.th = 0.02,
  verbose = 0
)

Arguments

cl	Cluster membership cluster
co.ratio	cell-cell co-clustering matrix.
cl.mat	cell-cluster matrix collected from bootstrapping iterations. Either co.ratio or cl.mat should not be NULL.
confusion.th	Clusters with average confusion score greater than this threshold will be removed. Cells in this cluster will be re-distributed to other most likely clusters.
min.cells	Clusters with fewer than this many cells will be removed. Cells in this cluster will be re-distributed to other most likely clusters.
niter	maxmimal mumber of refinement iterations.
tol.th	If improvement is smaller than this threshold, terminate refinement step.
verbose	If true, print out step-by-step improvement.

Author(s)

Zizhen Yao

AllenInstitute/scrattch.hicat documentation built on Oct. 20, 2023, 6:55 a.m.