get_pseudobulk {scITD}

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.