zinbwave_estimation | R Documentation |
This function is used to estimate useful parameters from a real dataset by
using zinbEstimate
function in Splatter package.
zinbwave_estimation(ref_data, verbose = FALSE, other_prior = NULL, seed)
ref_data |
A count matrix. Each row represents a gene and each column represents a cell. |
verbose |
Logical. |
other_prior |
A list with names of certain parameters. Some methods need
extra parameters to execute the estimation step, so you must input them. In
simulation step, the number of cells, genes, groups, batches, the percent of
DEGs are usually customed, so before simulating a dataset you must point it out.
See |
seed |
An integer of a random seed. |
In zinbwave, users do not input other extra information usually. If users want
to check the parameters, please see splatter::zinbEstimate()
or splatter::ZINBParams()
.
A list contains the estimated parameters and the results of execution detection.
Zappia L, Phipson B, Oshlack A. Splatter: simulation of single-cell RNA sequencing data. Genome biology, 2017, 18(1): 1-15. https://doi.org/10.1186/s13059-017-1305-0
Bioconductor URL: https://bioconductor.org/packages/release/bioc/html/splatter.html
Github URL: https://github.com/Oshlack/splatter
## Not run:
ref_data <- simmethods::data
## maybe it will take a long time
estimate_result <- simmethods::zinbwave_estimation(ref_data = ref_data,
other_prior = NULL,
verbose = TRUE,
seed = 111)
## End(Not run)
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