sc_clustering.simlr: Perform Single Cell data clustering using SIMLR

In pengminshi/MRtree: Multi-resolution Reconciled Tree

Perform Single Cell data clustering using SIMLR

Description

Perform Single Cell data clustering using SIMLR

Usage

sc_clustering.simlr(
  exprs,
  Ks,
  type = c("count", "log"),
  estimate.k = FALSE,
  scale.factor = 10^4,
  cores.ratio = 0.9,
  column.prefix = "simlr_"
)

Arguments

exprs	n.genes-by-n.cells expression matrix
Ks	vector of resolution, number of clusters
type	string, type of the expression matrix, choices are 'count' and 'log', and default by 'counts'
estimate.k	whether to estimate optimal number of clusters by SIMLR
scale.factor	scalar sets the scale factor for cell-level normalization
cores.ratio	ratio of total number of cores used for calculation
column.prefix	string, output column prefix, default 'simlr_'

Value

an SingleCellExperiment object containing all the clustering results

pengminshi/MRtree documentation built on March 6, 2023, 4:20 p.m.