RunICA: Run Independent Component Analysis on gene expression

In Seurat: Tools for Single Cell Genomics

Run Independent Component Analysis on gene expression

Description

Run fastica algorithm from the ica package for ICA dimensionality reduction. For details about stored ICA calculation parameters, see PrintICAParams.

Usage

RunICA(object, ...)

## Default S3 method:
RunICA(
  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,
  ...
)

## S3 method for class 'Assay'
RunICA(
  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,
  ...
)

## S3 method for class 'Seurat'
RunICA(
  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

object	Seurat object
...	Additional arguments to be passed to fastica
assay	Name of Assay ICA is being run on
nics	Number of ICs to compute
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).
ica.function	ICA function from ica package to run (options: icafast, icaimax, icajade)
verbose	Print the top genes associated with high/low loadings for the ICs
ndims.print	ICs to print genes for
nfeatures.print	Number of genes to print for each IC
reduction.name	dimensional reduction name
reduction.key	dimensional reduction key, specifies the string before the number for the dimension names.
seed.use	Set a random seed. Setting NULL will not set a seed.
features	Features to compute ICA on

Seurat documentation built on Nov. 18, 2023, 1:10 a.m.