sim_data

This dataset was generated in the "Generate Simulation Datasets" step in the Parametric_simulation.rmd (<a href="https://github.com/Lujun995/DiSC_Replication_Code">https://github.com/Lujun995/DiSC_Replication_Code</a>)

datasets

A suite of statistical methods for analysis of single-cell omics data including linear model-based methods for differential abundance analysis for individual level single-cell RNA-seq data. For more details see Zhang, et al. (Submitted to Bioinformatics)<https://github.com/Lujun995/DiSC_Replication_Code>.

Jun Chen

SingleCellStat

A Toolkit for Statistical Analysis of Single-Cell Omics Data

Lujun Zhang

sim_data function

It contains 12 cases and 12 controls, each with 375 cell replicates. The read depths of each cell replicate are well-balanced. A covariate called RIN (RNA Integrity Number) at the individual level is included in the dataset.
The dataset comprises a total of 1,000 genes. The signal density was 15%, with differences in mean, variance, and mean+variance (each at 5%). The ground truth of differential/equally expression genes are indicated by <code>gene_index</code>, including <code>mean_index</code> (genes with a difference in mean), <code>var_index</code> (genes with a difference in variance), <code>mean_var_index</code> (genes with a difference in both mean and variance), <code>EE_index</code> (otherwise (to estimate type-I error)).
A list of elements:
<dl>
 <dt><code>count_matrix</code></dt>
<dd>A numeric count matrix.</dd> <dt><code>meta_cell</code></dt>
<dd>A data.frame of the metadata at the cell level.</dd> <dt><code>meta_ind</code></dt>
<dd>A data.frame of the metadata at the individual level.</dd> <dt><code>gene_index</code></dt>
<dd>A list of 4 numeric vectors representing the ground truth of the IDs of the differentially or equally expressed genes.</dd> 
</dl>

Format

This dataset was generated in the "Generate Simulation Datasets" step in the Parametric_simulation.rmd (<a href='https://github.com/Lujun995/DiSC_Replication_Code'>https://github.com/Lujun995/DiSC_Replication_Code</a>)

Simulated Single-cell Sequencing Dataset — sim_data

It contains 12 cases and 12 controls, each with 375 cell replicates. The read depths of each cell replicate are well-balanced. A covariate called RIN (RNA Integrity Number) at the individual level is included in the dataset.
The dataset comprises a total of 1,000 genes. The signal density was 15%, with differences in mean, variance, and mean+variance (each at 5%). The ground truth of differential/equally expression genes are indicated by <code>gene_index</code>, including <code>mean_index</code> (genes with a difference in mean), <code>var_index</code> (genes with a difference in variance), <code>mean_var_index</code> (genes with a difference in both mean and variance), <code>EE_index</code> (otherwise (to estimate type-I error)).
A list of elements:
<dl>
 <dt><code>count_matrix</code></dt>
<dd>A numeric count matrix.</dd>

 <dt><code>meta_cell</code></dt>
<dd>A data.frame of the metadata at the cell level.</dd>

 <dt><code>meta_ind</code></dt>
<dd>A data.frame of the metadata at the individual level.</dd>

 <dt><code>gene_index</code></dt>
<dd>A list of 4 numeric vectors representing the ground truth of the IDs of the differentially or equally expressed genes.</dd>

 
</dl>

sim_data: Simulated Single-cell Sequencing Dataset

Description

Usage

Arguments

Format

Examples