generate_null: Generate null data

In linnykos/eSVD2: eSVD2 for performing the eSVD-DE for cohort-wide differential expression analysis

Generate null data

Description

This function doesn't allow of much flexbility, and is meant primarily for simple null simulations. Here, 'n' (the number of cells) is equal to 'cell_per_person*num_individuals'.

Usage

generate_null(cell_per_person = 100, num_genes = 1000, num_individuals = 20)

Arguments

cell_per_person	The number of cells per individual
num_genes	The number of genes in the simulation
num_individuals	The number of individuals

Value

a list with covariates (a 'matrix' with 'n' cells and 4 columns, named '"Intercept"', '"Log_UMI"', '"Sex"', and '"Age"', which will be used in 'eSVD2::initialize_esvd'), df (a 'data.frame' with 'num_individuals' rows and 5 columns, named named '"Intercept"', '"Log_UMI"', '"Sex"', '"Age"', and '"Individual"'), metadata_individual (a 'matrix' with 'n' rows and 1 column called '"Individual"' for which cell originates from which individual) nat_mat (a ‘n' by 'p' 'matrix' denoting the natural parameter for each cell’s gene expression), and obs_mat (a ‘n' by 'p' 'dgCMatrix' denoting the observed count for each cell’s gene expression),

linnykos/eSVD2 documentation built on July 17, 2024, 12:01 a.m.