bulkDimReduction {MOCHA} | R Documentation |
bulkDimReduction
Description
bulkDimReduction
runs dimensionality reduction (either PCA or LSI). We adapt Signac's
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
References
LSI method adapted from Andrew Hill: http://andrewjohnhill.com/blog/2019/05/06/dimensionality-reduction-for-scatac-data/
Examples
## Not run:
LSIObj <- MOCHA::bulkDimReduction(SampleTileObj, cellType = "CD16_Mono")
## End(Not run)