get_pseudobulk: Collapse data from cell-level to donor-level via summing...

In scITD: Single-Cell Interpretable Tensor Decomposition

Collapse data from cell-level to donor-level via summing counts. Generally, this should be done through calling the form_tensor() wrapper function.

Description

Collapse data from cell-level to donor-level via summing counts. Generally, this should be done through calling the form_tensor() wrapper function.

Usage

get_pseudobulk(container, shuffle = FALSE, shuffle_within = NULL)

Arguments

container	environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses
shuffle	logical Set to TRUE to shuffle cell-donor linkages (default=FALSE)
shuffle_within	character A metadata variable to shuffle cell-donor linkages within (default=NULL)

Value

The project container with pseudobulked count matrices in container$scMinimal_ctype$<ctype>$pseudobulk slots for each cell type.

scITD documentation built on Sept. 8, 2023, 5:11 p.m.