Run PCA or LSI dimensionality reduction on tiles
Source:R/dimensionalityReduction.R
bulkDimReduction.Rd
bulkDimReduction
runs dimensionality reduction (either PCA or LSI)
Usage
bulkDimReduction(
SampleTileObj,
cellType = "All",
componentNumber = 30,
method = "LSI",
verbose = FALSE
)
Arguments
- SampleTileObj
The SummarizedExperiment object output from getSampleTileMatrix
- cellType
vector of strings. Cell subsets for which to call peaks. This list of group names must be identical to names that appear in the SampleTileObj. Optional, if cellPopulations='ALL', then peak calling is done on all cell populations. Default is 'ALL'.
- componentNumber
integer. Number of components to include in LSI, or PCA This must be strictly less than
- method
a string. Represents the method to use. Includes LSI or PCA, but we do not recommend PCA for scATAC pseudobulk.
- verbose
Set TRUE to display additional messages. Default is FALSE.
Value
SEObj a SummarizedExperiment containing PC components from dimensionality reduction and metadata from the SampleTileObj