Seurat (version 1.2.1)

ica: Run Independent Component Analysis on gene expression

Description

Run fastICA algorithm for ICA dimensionality reduction

Usage

ica(object, ic.genes = NULL, do.print = TRUE, ics.print = 5, ics.store = 30, genes.print = 30, use.imputed = FALSE, seed.use = 1, ...)

Arguments

object

Seurat object

ic.genes

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

do.print

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

ics.print

Number of ICs to print genes for

ics.store

Number of ICs to store

genes.print

Number of genes to print for each IC

use.imputed

Run ICA on imputed values (FALSE by default)

seed.use

Random seed to use for fastICA

...

Additional arguments to be passed to fastICA

Value

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