Whats the role of "variable.features.n" in SCTransform function of Seurat? I try setting "variable.features.n" at three different numbers (2000, 5000, 10000). In the downstream cells are clustering in different groups?
variable.features.n sets the number of features (you can think of genes in the case of scRNA-seq) you would like to use for the downstream steps such as clustering. Basically, using a gene that is expressed more or less at similar levels across different cell types would not be informative in terms of differentiating (for example via clustering) these cell types, this parameter helps you to choose the "most informative" (most variable across the whole data set) features.