SRTsim_estimation: Estimate Parameters From Real Datasets by SRTsim

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

Estimate Parameters From Real Datasets by SRTsim

Description

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

Usage

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

Arguments

ref_data	A count matrix. Each row represents a gene and each column represents a cell/spot.
verbose	Logical.
other_prior	A list with names of certain parameters. Some methods need extra parameters to execute the estimation step, so you should input them. See Details below for more information.
seed	An integer of a random seed.

Details

In SRTsim, users should input the spatial coordinates of spots or cells in the spatial transcriptome data.

1. spatial.x. The x-axis coordinates.

2. spatial.y. The y-axis coordinates.

3. group.condition. Users can also input a numeric vector to specify the tissues or domains that each cell/spot comes from, like ⁠other_prior = list(group.condition = the numeric vector)⁠.

4. sim_scheme. If the labels of cells/spots represents the tissue layers or slices, sim_scheme should be set as tissue. sim_scheme is set as domain by default.

Value

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

References

Zhu J, Shang L, Zhou X. SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics. Genome Biology, 2023, 24(1): 39. https://doi.org/10.1186/s13059-023-02879-z

URL: https://cran.r-project.org/web/packages/SRTsim/index.html

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