CancerInSilico_estimation: Estimate Parameters From Real Datasets by CancerInSilico

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

Estimate Parameters From Real Datasets by CancerInSilico

Description

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

Usage

CancerInSilico_estimation(ref_data, verbose = FALSE, seed)

Arguments

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

Value

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

References

Sherman T D, Kagohara L T, Cao R, et al. CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. PLoS computational biology, 2019, 14(4): e1006935. https://doi.org/10.1371/journal.pcbi.1006935

Bioconductor URL: https://bioconductor.org/packages/release/bioc/html/CancerInSilico.html

Github URL: https://github.com/FertigLab/CancerInSilico

Examples

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

## End(Not run)

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