| normalize_pseudobulk {scITD} | R Documentation |
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.