CreateDimReducObject: Create a DimReduc object

In mojaveazure/seurat-object: Data Structures for Single Cell Data

Create a DimReduc object

Description

Create a DimReduc object

Usage

CreateDimReducObject(
  embeddings = new(Class = "matrix"),
  loadings = new(Class = "matrix"),
  projected = new(Class = "matrix"),
  assay = NULL,
  stdev = numeric(),
  key = NULL,
  global = FALSE,
  jackstraw = NULL,
  misc = list()
)

Arguments

embeddings	A matrix with the cell embeddings
loadings	A matrix with the feature loadings
projected	A matrix with the projected feature loadings
assay	Assay used to calculate this dimensional reduction
stdev	Standard deviation (if applicable) for the dimensional reduction
key	A character string to facilitate looking up features from a specific DimReduc
global	Specify this as a global reduction (useful for visualizations)
jackstraw	Results from the JackStraw function
misc	list for the user to store any additional information associated with the dimensional reduction

Value

A DimReduc object

See Also

Dimensional reduction object, validity, and interaction methods DimReduc-class, DimReduc-validity, [.DimReduc(), [[.DimReduc(), dim.DimReduc(), merge.DimReduc(), print.DimReduc(), subset.DimReduc()

Examples

data <- GetAssayData(pbmc_small[["RNA"]], slot = "scale.data")
pcs <- prcomp(x = data)
pca.dr <- CreateDimReducObject(
  embeddings = pcs$rotation,
  loadings = pcs$x,
  stdev = pcs$sdev,
  key = "PC",
  assay = "RNA"
)

mojaveazure/seurat-object documentation built on Dec. 13, 2024, 9:23 a.m.