https://github.com/satijalab/seurat
Tip revision: ff5e07bf8fc36d6e12c844be3a48d9ea6ad4be7a authored by David Collins on 07 May 2024, 21:04:23 UTC
Point Visium HD vignette to pre-release
Point Visium HD vignette to pre-release
Tip revision: ff5e07b
RunICA.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/generics.R, R/dimensional_reduction.R
\name{RunICA}
\alias{RunICA}
\alias{RunICA.default}
\alias{RunICA.Assay}
\alias{RunICA.Seurat}
\title{Run Independent Component Analysis on gene expression}
\usage{
RunICA(object, ...)
\method{RunICA}{default}(
object,
assay = NULL,
nics = 50,
rev.ica = FALSE,
ica.function = "icafast",
verbose = TRUE,
ndims.print = 1:5,
nfeatures.print = 30,
reduction.name = "ica",
reduction.key = "ica_",
seed.use = 42,
...
)
\method{RunICA}{Assay}(
object,
assay = NULL,
features = NULL,
nics = 50,
rev.ica = FALSE,
ica.function = "icafast",
verbose = TRUE,
ndims.print = 1:5,
nfeatures.print = 30,
reduction.name = "ica",
reduction.key = "ica_",
seed.use = 42,
...
)
\method{RunICA}{Seurat}(
object,
assay = NULL,
features = NULL,
nics = 50,
rev.ica = FALSE,
ica.function = "icafast",
verbose = TRUE,
ndims.print = 1:5,
nfeatures.print = 30,
reduction.name = "ica",
reduction.key = "IC_",
seed.use = 42,
...
)
}
\arguments{
\item{object}{Seurat object}
\item{\dots}{Additional arguments to be passed to fastica}
\item{assay}{Name of Assay ICA is being run on}
\item{nics}{Number of ICs to compute}
\item{rev.ica}{By default, computes the dimensional reduction on the cell x
feature matrix. Setting to true will compute it on the transpose (feature x cell
matrix).}
\item{ica.function}{ICA function from ica package to run (options: icafast,
icaimax, icajade)}
\item{verbose}{Print the top genes associated with high/low loadings for
the ICs}
\item{ndims.print}{ICs to print genes for}
\item{nfeatures.print}{Number of genes to print for each IC}
\item{reduction.name}{dimensional reduction name}
\item{reduction.key}{dimensional reduction key, specifies the string before
the number for the dimension names.}
\item{seed.use}{Set a random seed. Setting NULL will not set a seed.}
\item{features}{Features to compute ICA on}
}
\description{
Run fastica algorithm from the ica package for ICA dimensionality reduction.
For details about stored ICA calculation parameters, see
\code{PrintICAParams}.
}
\concept{dimensional_reduction}