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.
## Not run: # Load example data library(scater) data("sc_example_counts") conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE) params <- scDDEstimate(sc_example_counts, conditions = conditions) params ## End(Not run)