runSeuratFindClusters: runSeuratFindClusters Computes the clusters from the input...

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

runSeuratFindClusters Computes the clusters from the input sce object and stores them back in sce object

Description

runSeuratFindClusters Computes the clusters from the input sce object and stores them back in sce object

Usage

runSeuratFindClusters(
  inSCE,
  useAssay = "seuratNormData",
  useReduction = c("pca", "ica"),
  dims = 10,
  algorithm = c("louvain", "multilevel", "SLM"),
  groupSingletons = TRUE,
  resolution = 0.8,
  seed = 12345,
  externalReduction = NULL,
  verbose = TRUE
)

Arguments

inSCE	(sce) object from which clusters should be computed and stored in
useAssay	Assay containing scaled counts to use for clustering.
useReduction	Reduction method to use for computing clusters. One of "pca" or "ica". Default "pca".
dims	numeric value of how many components to use for computing clusters. Default 10.
algorithm	selected algorithm to compute clusters. One of "louvain", "multilevel", or "SLM". Use louvain for "original Louvain algorithm" and multilevel for "Louvain algorithm with multilevel refinement". Default louvain.
groupSingletons	boolean if singletons should be grouped together or not. Default TRUE.
resolution	Set the resolution parameter to find larger (value above 1) or smaller (value below 1) number of communities. Default 0.8.
seed	Specify the seed value. Default 12345.
externalReduction	Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.
verbose	Logical value indicating if informative messages should be displayed. Default is TRUE.

Value

Updated sce object which now contains the computed clusters

Examples

data(scExample, package = "singleCellTK")
## Not run: 
sce <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")
sce <- runSeuratPCA(sce, useAssay = "counts")
sce <- runSeuratFindClusters(sce, useAssay = "counts")

## End(Not run)

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.