ProjectDim: Project Dimensional reduction onto full dataset

In mayer-lab/SeuratForMayer2018: Seurat : R Toolkit for Single Cell Genomics

Description

Takes a pre-computed dimensional reduction (typically calculated on a subset of genes) and projects this onto the entire dataset (all genes). Note that the cell loadings will remain unchanged, but now there are gene loadings for all genes.

Usage

ProjectDim(object, reduction.type = "pca", dims.print = 1:5,
  dims.store = 30, genes.print = 30, replace.dim = FALSE,
  do.center = FALSE, do.print = TRUE, assay.type = "RNA")

Arguments

object	Seurat object
reduction.type	Reduction to use
dims.print	Number of dims to print genes for
dims.store	Number of dims to store (default is 30)
genes.print	Number of genes with highest/lowest loadings to print for each PC
replace.dim	Replace the existing data (overwrite object@dr$[e-mail]), not done by default.
do.center	Center the dataset prior to projection (should be set to TRUE)
do.print	Print top genes associated with the projected dimensions
assay.type	Data type, RNA by default. Can be changed for multimodal datasets (i.e. project a PCA done on RNA, onto CITE-seq data)

Value

Returns Seurat object with the projected values in object@dr$[e-mail]

mayer-lab/SeuratForMayer2018 documentation built on May 25, 2019, 9:34 p.m.