PROSSTT_estimation: Estimate Parameters From Real Datasets by PROSSTT

In duohongrui/simmethods: A collection of 40+ simulation methods for singlce-cell RNA seqencing data

Estimate Parameters From Real Datasets by PROSSTT

Description

This function is used to estimate useful parameters from a real dataset by using make_trees function in simutils package.

Usage

PROSSTT_estimation(ref_data, other_prior = NULL, verbose = FALSE, seed)

Arguments

ref_data	A count matrix. Each row represents a gene and each column represents a cell.
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 Details below for more information.
verbose	Logical.
seed	An integer of a random seed.

Details

In PROSSTT, users can input cell group information by other_prior = list(group.condition = xxx). If this information is not available, we will detect the potential groups in reference data automatically. For more information about PROSSTT, see Examples and References.

Value

A list contains the estimated parameters and the results of execution detection.

References

Papadopoulos N, Gonzalo P R, Söding J. PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes. Bioinformatics, 2019, 35(18): 3517-3519. https://doi.org/10.1093/bioinformatics/btz078

Github URL: https://github.com/soedinglab/prosstt/

Document URL: http://wwwuser.gwdg.de/~compbiol/prosstt/doc/

Examples

## Not run: 
ref_data <- simmethods::data
## estimation
estimate_result <- simmethods::PROSSTT_estimation(
  ref_data = ref_data,
  other_prior = NULL,
  verbose = TRUE,
  seed = 111
)

## End(Not run)

duohongrui/simmethods documentation built on June 17, 2024, 10:49 a.m.