ICA: Run Independent Component Analysis on gene expression

In nukappa/seurat_v2: Seurat : R toolkit for single cell genomics

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]]

nukappa/seurat_v2 documentation built on May 24, 2019, 9:57 a.m.