iter_nmf: Run iterative NMF for K=2 until it cannot no longer separate...

In naikai/sake: Single-cell RNA-Seq Analysis and Klustering Evaluation

Run iterative NMF for K=2 until it cannot no longer separate samples

Description

Run iterative NMF for K=2 until it cannot no longer separate samples

Usage

iter_nmf(rawdata, nrun = 10, round = 1, min.sample = 10,
  mad = 5000, silhouette = 0.95, w.silhouette = 0.7,
  w.min.sample = 10, ncores = 8)

Arguments

rawdata	gene count table
nrun	number of runs for each NMF
min.sample	number of required minimum samples in each subclusters
mad	number of top MAD genes
silhouette	min required threshold for silhouette index after NMF run

Examples

iter_nmf(rawdata, nrun=10, mad=5000)

naikai/sake documentation built on Feb. 15, 2023, 11 p.m.