unsupervisedAnalysisSc-DsATACsc-method: unsupervisedAnalysisSc-methods

In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

unsupervisedAnalysisSc-methods

Description

Perform unsupervised analysis on single-cell data. Performs dimensionality reduction and clustering.

Usage

## S4 method for signature 'DsATACsc'
unsupervisedAnalysisSc(
  .object,
  regionType,
  regionIdx = NULL,
  dimRedMethod = "tf-idf_irlba",
  usePcs = 1:50,
  clusteringMethod = "seurat_louvain"
)

Arguments

.object	DsATACsc object
regionType	character string specifying the region type
regionIdx	indices of regions to be used (logical or integer vector). If NULL (default) all regions of the specified regionType will be used.
dimRedMethod	character string specifying the dimensionality reduction method. Currently on "tf-idf_irlba" is supported
usePcs	integer vector specifying the principal components to use for UMAP and clustering
clusteringMethod	character string specifying the clustering method. Currently on "seurat_louvain" is supported

Value

an S3 object containing dimensionality reduction results and clustering

Author(s)

Fabian Mueller

GreenleafLab/ChrAccR documentation built on March 22, 2023, 11:42 p.m.