MOCHA (version 1.1.0)

bulkDimReduction: 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
)

Value

SEObj a SummarizedExperiment containing PC components from dimensionality reduction and metadata from the SampleTileObj

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.

References

LSI method adapted from Andrew Hill: http://andrewjohnhill.com/blog/2019/05/06/dimensionality-reduction-for-scatac-data/

Examples

if (FALSE) {
LSIObj <- MOCHA::bulkDimReduction(SampleTileObj, cellType = "CD16_Mono")
}