Run Independent Component Analysis on gene expression
Run fastica algorithm from the ica package for ICA dimensionality reduction.
For details about stored ICA calculation parameters, see
PrintICAParams.
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, ... )
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 |
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