RunICA: 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, ...)
# S3 method for default
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 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 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