Estimate simulation parameters for the scDD simulation from a real dataset.
scDDEstimate(counts, conditions, params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam()) # S3 method for SCESet scDDEstimate(counts, conditions, params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam()) # S3 method for matrix scDDEstimate(counts, conditions, params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam())
counts | either a counts matrix or an SCESet object containing count data to estimate parameters from. |
---|---|
conditions | Vector giving the condition that each cell belongs to. Conditions can be 1 or 2. |
params | SCDDParams object to store estimated values in. |
verbose | logical. Whether to show progress messages. |
BPPARAM | A |
SCDDParams object containing the estimated parameters.
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.
# NOT RUN { data("sc_example_counts") conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE) params <- scDDEstimate(sc_example_counts, conditions) params # }