Seurat (version 1.2.1)

pca: Run Principal Component Analysis on gene expression

Description

Run prcomp for PCA dimensionality reduction

Usage

pca(object, pc.genes = NULL, do.print = TRUE, pcs.print = 5, pcs.store = 40, genes.print = 30, use.imputed = FALSE, ...)

Arguments

object

Seurat object

pc.genes

Genes to use as input for PCA. Default is [e-mail]

do.print

Print the top genes associated with high/low loadings for the PCs

pcs.print

Number of PCs to print genes for

pcs.store

Number of PCs to store

genes.print

Number of genes to print for each PC

use.imputed

Run PCA on imputed values (FALSE by default)

...

Additional arguments to be passed to prcomp

Value

Returns Seurat object with an PCA embedding ([e-mail]) and gene projection matrix (object@pca.x). The PCA object itself is stored in [e-mail][[1]]