BestMatchParams: Get the best matched parameter

In YosefLab/SymSim: Simulate Single Cell RNA Sequencing Data

Get the best matched parameter

Description

This function matches a real dataset to a database of summary information of simulated datasets, plots a qqplot for user to visualize similarity between their dataset and the simulated dataset, and suggests parameters to use in the simulation

Usage

BestMatchParams(
  tech,
  counts,
  plotfilename,
  n_optimal = 3,
  depth_range = c(-Inf, Inf),
  alpha_range = c(-Inf, Inf),
  idx_set = NULL
)

Arguments

tech	'nonUMI','UMI' the match database are constructed based on reasonable values for each technology
counts	expression matrix
plotfilename	output name for qqplot
n_optimal	number of top parameter configurations to return
depth_range	if one knows the rough range of sequencing depth, it can be input here.
alpha_range	if one knows the rough range of mRNA capture efficiency, it can be input here.

Value

three set of best matching parameters that was used to simulate the best matching dataset to the experimental dataset

YosefLab/SymSim documentation built on Sept. 30, 2024, 2:22 p.m.