subsetCeldaList: Subset celda model from SCE object returned from...

In campbio/celda: CEllular Latent Dirichlet Allocation

Subset celda model from SCE object returned from celdaGridSearch

Description

Select a subset of models from a SingleCellExperiment object generated by celdaGridSearch that match the criteria in the argument params.

Usage

subsetCeldaList(x, params, altExpName = "featureSubset")

## S4 method for signature 'SingleCellExperiment'
subsetCeldaList(x, params, altExpName = "featureSubset")

## S4 method for signature 'celdaList'
subsetCeldaList(x, params)

Arguments

x	Can be one of A SingleCellExperiment object returned from celdaGridSearch, recursiveSplitModule, or recursiveSplitCell. Must contain a list named "celda_grid_search" in metadata(x). celdaList object.
params	List. List of parameters used to subset the matching celda models in list "celda_grid_search" in metadata(x).
altExpName	The name for the altExp slot to use. Default "featureSubset".

Value

One of

• A new SingleCellExperiment object containing all models matching the provided criteria in params. If only one celda model result in the "celda_grid_search" slot in metadata(x) matches the given criteria, a new SingleCellExperiment object with the matching model stored in the metadata "celda_parameters" slot will be returned. Otherwise, a new SingleCellExperiment object with the subset models stored in the metadata "celda_grid_search" slot will be returned.

• A new celdaList object containing all models matching the provided criteria in params. If only one item in the celdaList matches the given criteria, the matching model will be returned directly instead of a celdaList object.

See Also

celdaGridSearch can run Celda with multiple parameters and chains in parallel. selectBestModel can get the best model for each combination of parameters.

Examples

data(sceCeldaCGGridSearch)
sceK5L10 <- subsetCeldaList(sceCeldaCGGridSearch,
    params = list(K = 5, L = 10))
data(celdaCGGridSearchRes)
resK5L10 <- subsetCeldaList(celdaCGGridSearchRes,
    params = list(K = 5, L = 10))

campbio/celda documentation built on April 5, 2024, 11:47 a.m.