dot-defineSubspace: .defineSubspace

In CellMixS: Evaluate Cellspecific Mixing

Description

Helper function for ldfSce and cms to define or recalculate the subspace for analysis.

Usage

.defineSubspace(sce, assay_name, dim_red, n_dim)

Arguments

sce	A SingleCellExperiment object with the data to define the subspace.
assay_name	Character. Name of the assay to use for PCA. Only relevant if no existing 'dim_red' is provided. Must be one of names(assays(sce)).
dim_red	Character. Name of embeddings to use as subspace.
n_dim	Numeric. Number of subspace elements to include to define subspace.

Details

Function to determine the subspace for ldfDiff and cms. Checks whether the defined 'dim_red' is present. Only if no subspace is defined or present it will perform a PCA using runPCA. To calculate PCA counts defined in 'assay_name' are used.

Value

A matrix of cell embeddings with reduced dimensions as columns.

See Also

ldfSce, cms.

Other helper functions: .cmsCell(), .filterKnn(), .filterLocMin(), .ldfKnn(), .smoothCms()

CellMixS documentation built on Dec. 19, 2020, 2 a.m.