sparseDCEstimate {splatter} | R Documentation |
Estimate simulation parameters for the SparseDC simulation from a real dataset.
sparseDCEstimate( counts, conditions, nclusters, norm = TRUE, params = newSparseDCParams() ) ## S3 method for class 'SingleCellExperiment' sparseDCEstimate( counts, conditions, nclusters, norm = TRUE, params = newSparseDCParams() ) ## S3 method for class 'matrix' sparseDCEstimate( counts, conditions, nclusters, norm = TRUE, params = newSparseDCParams() )
counts |
either a counts matrix or an SingleCellExperiment object containing count data to estimate parameters from. |
conditions |
numeric vector giving the condition each cell belongs to. |
nclusters |
number of cluster present in the dataset. |
norm |
logical, whether to library size normalise counts before estimation. Set this to FALSE if counts is already normalised. |
params |
PhenoParams object to store estimated values in. |
The nGenes
and nCells
parameters are taken from the size of the
input data. The counts are preprocessed using
pre_proc_data
and then parameters are estimated using
sparsedc_cluster
using lambda values calculated using
lambda1_calculator
and
lambda2_calculator
.
See SparseDCParams
for more details on the parameters.
SparseParams object containing the estimated parameters.
if (requireNamespace("SparseDC", quietly = TRUE)) { # Load example data library(scater) set.seed(1) sce <- mockSCE(ncells = 20, ngenes = 100) conditions <- sample(1:2, ncol(sce), replace = TRUE) params <- sparseDCEstimate(sce, conditions, nclusters = 3) params }