two_batch_matrix: Simulated count matrix from two batches

In jichunxie/CDI: Clustering Deviation Index (CDI)

Simulated count matrix from two batches

Description

This matrix contains raw UMI count matrix simulated from the Negative Binomial(NB) mixture distribution. The code simulating this vector can be found in data-raw/two_batch_simulation.R.

Usage

data(two_batch_matrix)

Format

A matrix with 3,000 genes (rows) and 2,000 cells (columns). The cells are from 5 cell type, and each cell type contains 400 cells. Within each cell type, 200 of cells with odd indices are from batch 1, and the other cells with even indices are from batch 2. See Note for details of simulation setting.

Note

We first simulated one batch of cells with 1,000 cells in total. Within the batch, we simulated 3,000 genes and five group of cells with 400 cells each. One group of cells was treated as the baseline group. The mean parameters are generated from truncated Normal with mean and standard deviation 0.2, 0.1 and dispersion generated from truncated with mean and standard deviation 0.5, 0.1. For each of the other four groups, 30 genes had mean parameters shifted from the baseline group with log2 fold change 2.5. Dispersion parameters of feature genes were shifted by a normalized factor with mean 0 and standard deviation 0.05. To generate the second batch of cells, we shifted the mean parameters of randomly selected 10

jichunxie/CDI documentation built on Dec. 6, 2023, 5:48 a.m.