check_norm: check if select norm method is an available option

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

check if select norm method is an available option

Description

check if select norm method is an available option

Usage

check_norm(vesalius_assay, norm_method, method = NULL, verbose = TRUE)

Arguments

vesalius_assay	a vesalius_assay
norm_method	string - selected normalisation parsed by user
method	DEG method
verbose	logical if progress message should be ouputed

Details

Here we check if the normalisation method has been computed in the count slot. We also check if this is used in the context of differential gene expression analysis. DESeq and edgeR require raw counts so if the user parses a valid norm method but is running DEG with one those methods, we ignore request and parse raw count instead.

Value

count matrix

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.