https://github.com/satijalab/seurat
Tip revision: 7369248c139783ad906aad1f8ca4e6ebab0d004a authored by Andrew Butler on 27 July 2017, 00:52:21 UTC
update version to release 2.0
update version to release 2.0
Tip revision: 7369248
RunICA.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/dimensional_reduction.R
\name{RunICA}
\alias{RunICA}
\title{Run Independent Component Analysis on gene expression}
\usage{
RunICA(object, ic.genes = NULL, ics.compute = 50, use.imputed = FALSE,
rev.ica = FALSE, print.results = TRUE, ics.print = 1:5,
genes.print = 50, ica.function = "icafast", seed.use = 1, ...)
}
\arguments{
\item{object}{Seurat object}
\item{ic.genes}{Genes to use as input for ICA. Default is object@var.genes}
\item{ics.compute}{Number of ICs to compute}
\item{use.imputed}{Run ICA on imputed values (FALSE by default)}
\item{rev.ica}{By default, computes the dimensional reduction on the cell x
gene matrix. Setting to true will compute it on the transpose (gene x cell
matrix).}
\item{print.results}{Print the top genes associated with each dimension}
\item{ics.print}{ICs to print genes for}
\item{genes.print}{Number of genes to print for each IC}
\item{ica.function}{ICA function from ica package to run (options: icafast,
icaimax, icajade)}
\item{seed.use}{Random seed to use for fastica}
\item{\dots}{Additional arguments to be passed to fastica}
}
\value{
Returns Seurat object with an ICA calculation stored in
object@dr$ica
}
\description{
Run fastica algorithm from the ica package for ICA dimensionality reduction.
For details about stored ICA calculation parameters, see
\code{\link{PrintICAParams}}.
}