hierarchicell: hierarchicell: A package for simulating cell-type specific...

In kdzimm/hierarchicell: Simulating Cell-Type Specific and Hierarchical Single-Cell RNA-Seq Data

Description

The hierarchicell package estimates important parameters from single-cell RNAseq expression counts before simulating expression data that is cell-type specific and hierarchical in nature. With the simulated data, hierarchicell is then able to compute power calculations under a variety of conditions. The package consists of four important categories of functions: data loading and cleaning, empirical estimation of distributions, simulating expression data, and computing type 1 error or power.

Data loading and filtering function

The data loading and cleaning function is very basic, but data input is critical to the package working correctly. If no input data is given, the package default data will be used for simulation and power calculations. For more detailed information see: filter_counts

Empirical estimation of distributions

The most fundamental component of this package is in the estimation of the simulation parameters. The functions to estimate parameters for the simulation estimate the empirical distributions for library size, dropout rate, and global gene means and model the hierarchical variance structure of the input data. For more detailed information see: empirical_estimation

Simulating expression data

With the parameters estimated, the package can simulate data under a variety of pre-determined conditions. These conditions include foldchange, number of genes, number of samples (i.e., independent experimental units), and the mean number of cells per individual. For more detailed information see: simulate_count_matrix

Computing type I error

With the parameters estimated, the package can compute type 1 error rates for a number of different tools under a variety of pre-determined conditions. These conditions include number of genes, number of samples (i.e., independent experimental units), and the mean number of cells per individual. For more detailed information see: compute_error

Computing power

With the parameters estimated, the package can compute power under a variety of pre-determined conditions. These conditions include foldchange, number of genes, number of samples (i.e., independent experimental units), and the mean number of cells per individual. For more detailed information see: compute_power

kdzimm/hierarchicell documentation built on Dec. 21, 2021, 5:23 a.m.