CreateDimReducObject: Create a DimReduc object

Description Usage Arguments Examples

View source: R/objects.R

Description

Create a DimReduc object

Usage

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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

Examples

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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"
)

Seurat documentation built on Jan. 13, 2021, 7:11 p.m.