aspecc: Spectral clustering.

In charliex210/sctools: Tools for single cell RNAseq analysis

Description

Clustering cells based on adaptive gauss kernel.

Usage

aspecc(Dist, numk = NULL, ka = 10, kNN = NULL, type = 3,
  estimateRage = 3:8, scaleDist = TRUE)

Arguments

Dist	Paire-wised distance matrix.
numk	Number of clusters number. If NULL, estimate number will be used.
ka	To equalize the number of neighbors we set the value sigma(i) for each cell i to the distance to its kath nearest neighbor. Default is 10.
kNN	Additional affinities beyond Kth nearest neighbor are set to zero. If NULL, kNN will be set the 3ka.
type	The variants of spectral clustering to use, see spectralClustering.
estimateRage	Estimate range.
scaleDist	scale distance.

Value

Spectral clustering labels, and affinity matrix.

References

David van Dijk et al. MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data. BioRxiv 2017.

Bo Wang et al. Similarity network fusion for aggregating data types on a genomic scale. Nature Methods 2014.

charliex210/sctools documentation built on Dec. 29, 2021, 11:19 p.m.