RunICA: Run Independent Component Analysis on gene expression
In satijalab/seurat: Tools for Single Cell Genomics

RunICA

R Documentation

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