unsupervisedAnalysisSc-methods

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

# S4 method for 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

Fabian Mueller