pca: Run Principal Component Analysis on gene expression

Description

Run prcomp for PCA dimensionality reduction

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

object

Seurat object

pc.genes

Genes to use as input for PCA. Default is [email protected]

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

Returns Seurat object with an PCA embedding ([email protected]) and gene projection matrix ([email protected]). The PCA object itself is stored in [email protected][[1]]