normalize_pseudobulk: Normalize the pseudobulked counts matrices. Generally, this...

In scITD: Single-Cell Interpretable Tensor Decomposition

Normalize the pseudobulked counts matrices. Generally, this should be done through calling the form_tensor() wrapper function.

Description

Normalize the pseudobulked counts matrices. Generally, this should be done through calling the form_tensor() wrapper function.

Usage

normalize_pseudobulk(container, method = "trim", scale_factor = 10000)

Arguments

container	environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses
method	character The normalization method to use on the pseudobulked count data. Set to 'regular' to do standard normalization of dividing by library size. Set to 'trim' to use edgeR trim-mean normalization, whereby counts are divided by library size times a normalization factor. (default='trim')
scale_factor	numeric The number that gets multiplied by fractional counts during normalization of the pseudobulked data (default=10000)

Value

The project container with normalized pseudobulk matrices in container$scMinimal_ctype$<ctype>$pseudobulk slots.

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