CreateDimReducObject: Create a DimReduc object

Description Usage Arguments Examples

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, 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

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")

atakanekiz/Seurat3.0 documentation built on May 26, 2019, 2:33 a.m.