compute_error: Computing Type 1 Error for Single Cell Expression...

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

Description

Computes type 1 error for single cell data that is cell-type specifc, hierarchical, and compositonal. This function computes type 1 error with the single-cell differential expression analysis tool 'MAST', using random effects to account for the correlation structure that exists among measures from cells within an individual. The type 1 error calculations will borrow information from the input data (or the package default data) to 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.

Details

Prior to running the error_hierarchicell function, it is important to run the filter_counts function followed by the compute_data_summaries function to build an R object that is in the right format for the following simulation function to properly work.

Note

Data should be only for cells of the specific cell-type you are interested in simulating or computing type 1 error for. Data should also contain as many unique sample identifiers as possible. If you are inputing data that has less than 5 unique values for sample identifier (i.e., independent experimental units), then the empirical estimation of the inter-individual heterogeneity is going to be very unstable. Finding such a dataset will be difficult at this time, but, over time (as experiments grow in sample size and the numbers of publically available single-cell RNAseq datasets increase), this should improve dramatically.

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