VeloSim_simulation | R Documentation |
Simulate Datasets by VeloSim
VeloSim_simulation(
parameters,
other_prior = NULL,
return_format,
verbose = FALSE,
seed
)
parameters |
A object generated by |
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 and other variables are usually customed, so before simulating a dataset you must point it out. |
return_format |
A character. Alternatives choices: list, SingleCellExperiment, Seurat, h5ad |
verbose |
Logical. Whether to return messages or not. |
seed |
A random seed. |
In VeloSim, users can only set nCells
and nGenes
to specify the number of cells and genes in the
simulated dataset. See Examples
for instructions.
Zhang Z, Zhang X. VeloSim: Simulating single cell gene-expression and RNA velocity. BioRxiv, 2021. https://doi.org/10.1101/2021.01.11.426277
Github URL: https://github.com/PeterZZQ/VeloSim
## Not run:
ref_data <- simmethods::data
## estimation with cell group information
group_condition <- paste0("Group", as.numeric(simmethods::group_condition))
estimate_result <- simmethods::VeloSim_estimation(
ref_data = ref_data,
other_prior = list(group.condition = group_condition),
verbose = TRUE,
seed = 111
)
# 1) Simulate with default parameters
simulate_result <- simmethods::VeloSim_simulation(
parameters = estimate_result[["estimate_result"]],
other_prior = NULL,
return_format = "list",
verbose = TRUE,
seed = 111
)
## counts
counts <- simulate_result[["simulate_result"]][["count_data"]]
dim(counts)
# 2) 200 cells and 5000 genes
simulate_result <- simmethods::VeloSim_simulation(
parameters = estimate_result[["estimate_result"]],
other_prior = list(nCells = 200,
nGenes = 5000),
return_format = "list",
verbose = TRUE,
seed = 111
)
## counts
counts <- simulate_result[["simulate_result"]][["count_data"]]
dim(counts)
## End(Not run)
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