Clusters the rows of a count matrix containing single-cell data
into L modules. The
useAssay assay slot in
altExpName altExp slot will be used if
it exists. Otherwise, the useAssay
assay slot in x will be used if
x is a SingleCellExperiment object.
celda_G( x, useAssay = "counts", altExpName = "featureSubset", L, beta = 1, delta = 1, gamma = 1, stopIter = 10, maxIter = 200, splitOnIter = 10, splitOnLast = TRUE, seed = 12345, nchains = 3, yInitialize = c("split", "random", "predefined"), countChecksum = NULL, yInit = NULL, logfile = NULL, verbose = TRUE ) # S4 method for SingleCellExperiment celda_G( x, useAssay = "counts", altExpName = "featureSubset", L, beta = 1, delta = 1, gamma = 1, stopIter = 10, maxIter = 200, splitOnIter = 10, splitOnLast = TRUE, seed = 12345, nchains = 3, yInitialize = c("split", "random", "predefined"), countChecksum = NULL, yInit = NULL, logfile = NULL, verbose = TRUE ) # S4 method for ANY celda_G( x, useAssay = "counts", altExpName = "featureSubset", L, beta = 1, delta = 1, gamma = 1, stopIter = 10, maxIter = 200, splitOnIter = 10, splitOnLast = TRUE, seed = 12345, nchains = 3, yInitialize = c("split", "random", "predefined"), countChecksum = NULL, yInit = NULL, logfile = NULL, verbose = TRUE )
| x | A SingleCellExperiment
with the matrix located in the assay slot under |
|---|---|
| useAssay | A string specifying the name of the assay slot to use. Default "counts". |
| altExpName | The name for the altExp slot to use. Default "featureSubset". |
| L | Integer. Number of feature modules. |
| beta | Numeric. Concentration parameter for Phi. Adds a pseudocount to each feature module in each cell. Default 1. |
| delta | Numeric. Concentration parameter for Psi. Adds a pseudocount to each feature in each module. Default 1. |
| gamma | Numeric. Concentration parameter for Eta. Adds a pseudocount to the number of features in each module. Default 1. |
| stopIter | Integer. Number of iterations without improvement in the log likelihood to stop inference. Default 10. |
| maxIter | Integer. Maximum number of iterations of Gibbs sampling to perform. Default 200. |
| splitOnIter | Integer. On every `splitOnIter` iteration, a heuristic will be applied to determine if a feature module should be reassigned and another feature module should be split into two clusters. To disable splitting, set to -1. Default 10. |
| splitOnLast | Integer. After `stopIter` iterations have been performed without improvement, a heuristic will be applied to determine if a cell population should be reassigned and another cell population should be split into two clusters. If a split occurs, then `stopIter` will be reset. Default TRUE. |
| seed | Integer. Passed to with_seed. For reproducibility, a default value of 12345 is used. If NULL, no calls to with_seed are made. |
| nchains | Integer. Number of random cluster initializations. Default 3. |
| yInitialize | Chararacter. One of 'random', 'split', or 'predefined'. With 'random', features are randomly assigned to a modules. With 'split', features will be split into sqrt(L) modules and then each module will be subsequently split into another sqrt(L) modules. With 'predefined', values in `yInit` will be used to initialize `y`. Default 'split'. |
| countChecksum | Character. An MD5 checksum for the `counts` matrix. Default NULL. |
| yInit | Integer vector. Sets initial starting values of y. `yInit` can only be used when `yInitialize = 'predefined'`. Default NULL. |
| logfile | Character. Messages will be redirected to a file named
|
| verbose | Logical. Whether to print log messages. Default TRUE. |
A SingleCellExperiment object. Function
parameter settings are stored in the metadata
"celda_parameters" slot. Column celda_feature_module in
rowData contains feature modules.
celda_C for cell clustering and celda_CG for simultaneous clustering of features and cells. celdaGridSearch can be used to run multiple values of L and multiple chains in parallel.
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