SeuratObject (version 5.0.2)

CreateDimReducObject: 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()
)

Value

A DimReduc object

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

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"
)