scDDEstimate {splatter} | R Documentation |
Estimate simulation parameters for the scDD simulation from a real dataset.
scDDEstimate( counts, params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam(), ... ) ## S3 method for class 'matrix' scDDEstimate( counts, params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam(), conditions, ... ) ## S3 method for class 'SingleCellExperiment' scDDEstimate( counts, params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam(), condition = "condition", ... ) ## Default S3 method: scDDEstimate( counts, params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam(), condition, ... )
counts |
either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from. |
params |
SCDDParams object to store estimated values in. |
verbose |
logical. Whether to show progress messages. |
BPPARAM |
A |
... |
further arguments passed to or from other methods. |
conditions |
Vector giving the condition that each cell belongs to. Conditions can be 1 or 2. |
condition |
String giving the column that represents biological group of interest. |
This function applies preprocess
to the counts then uses
scDD
to estimate the numbers of each gene type to
simulate. The output is then converted to a SCDDParams object. See
preprocess
and scDD
for details.
SCDDParams object containing the estimated parameters.
if (requireNamespace("scDD", quietly = TRUE)) { library(scater) set.seed(1) sce <- mockSCE(ncells = 20, ngenes = 100) colData(sce)$condition <- sample(1:2, ncol(sce), replace = TRUE) params <- scDDEstimate(sce, condition = "condition") params }