How to regress dissociation-associated genes' effect by using ScaleData()?

[0106WeiWeiDeng]

Hi, all

Because experimental procedures (for instance, flow cytometry sorting) hurt some cells, I want to regress dissociation-associated genes' effect (or other gene sets') before running PCA, UMAP function. The method I use is showing below:

> all.genes <- rownames(x = lyy) # lyy is a seurat object
> gene.set <- readRDS(file = "gene_set.rds") # get gene name list
> all.genes <- all.genes[!tolower(all.genes) %in% tolower(gene.set)] # wipe off relate genes
> lyy <- ScaleData(object = lyy, features = all.genes)
> lyy <- RunPCA(object = lyy, features = VariableFeatures(object = lyy))

Is it correct? Please post your advice.