Run a supervised LSI (SLSI) dimensionality reduction supervised by a cell-cell kernel. SLSI is used to capture a linear transformation of peaks that maximizes its dependency to the given cell-cell kernel.
Usage
RunSLSI(object, ...)
# Default S3 method
RunSLSI(
object,
assay = NULL,
n = 50,
reduction.key = "SLSI_",
graph = NULL,
verbose = TRUE,
seed.use = 42,
...
)
# S3 method for class 'Assay'
RunSLSI(
object,
assay = NULL,
features = NULL,
n = 50,
reduction.key = "SLSI_",
graph = NULL,
verbose = TRUE,
seed.use = 42,
...
)
# S3 method for class 'StdAssay'
RunSLSI(
object,
assay = NULL,
features = NULL,
n = 50,
reduction.key = "SLSI_",
graph = NULL,
layer = "data",
verbose = TRUE,
seed.use = 42,
...
)
# S3 method for class 'Seurat'
RunSLSI(
object,
assay = NULL,
features = NULL,
n = 50,
reduction.name = "slsi",
reduction.key = "SLSI_",
graph = NULL,
verbose = TRUE,
seed.use = 42,
...
)Arguments
- object
An object
- ...
Arguments passed to IRLBA irlba
- assay
Name of Assay SLSI is being run on
- n
Total Number of SLSI components to compute and store
- reduction.key
dimensional reduction key, specifies the string before the number for the dimension names
- graph
Graph used supervised by SLSI
- verbose
Display messages
- seed.use
Set a random seed. Setting NULL will not set a seed.
- features
Features to compute SLSI on. If features=NULL, SLSI will be run using the variable features for the Assay5.
- layer
Layer to run SLSI on
- reduction.name
dimensional reduction name