Estimate simulation parameters for the BASiCS simulation from a real dataset.
BASiCSEstimate(counts, spike.info = NULL, batch = NULL, n = 20000, thin = 10, burn = 5000, regression = TRUE, params = newBASiCSParams(), verbose = TRUE, progress = TRUE, ...) # S3 method for SingleCellExperiment BASiCSEstimate(counts, spike.info = NULL, batch = NULL, n = 20000, thin = 10, burn = 5000, regression = TRUE, params = newBASiCSParams(), verbose = TRUE, progress = TRUE, ...) # S3 method for matrix BASiCSEstimate(counts, spike.info = NULL, batch = NULL, n = 20000, thin = 10, burn = 5000, regression = TRUE, params = newBASiCSParams(), verbose = TRUE, progress = TRUE, ...)
counts | either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from. |
---|---|
spike.info | data.frame describing spike-ins with two columns: "Name"
giving the names of the spike-in features (must match
|
batch | vector giving the batch that each cell belongs to. |
n | total number of MCMC iterations. Must be |
thin | thining period for the MCMC sampler. Must be |
burn | burn-in period for the MCMC sampler. Must be in the range
|
regression | logical. Whether to use regression to identify
over-dispersion. See |
params | BASiCSParams object to store estimated values in. |
verbose | logical. Whether to print progress messages. |
progress | logical. Whether to print additional BASiCS progress messages. |
... | Optional parameters passed to |
BASiCSParams object containing the estimated parameters.
This function is just a wrapper around BASiCS_MCMC
that
takes the output and converts it to a BASiCSParams object. Either a set of
spike-ins or batch information (or both) must be supplied. If only batch
information is provided there must be at least two batches. See
BASiCS_MCMC
for details.
# NOT RUN { # Load example data library(scater) data("sc_example_counts") spike.info <- data.frame(Name = rownames(sc_example_counts)[1:10], Input = rnorm(10, 500, 200), stringsAsFactors = FALSE) params <- BASiCSEstimate(sc_example_counts[1:100, 1:30], spike.info) params # }