I would like to see a more precise definition of vars_use in the software documentation. I understand that the purpose of it is to specify sources of unwanted variation (e.g. Chromium 3' versus Chromium 5'). However, a colleague of mine thinks that variables of wanted variation, such as smoker versus non-smoker, should be specified to vars_use. A clear sentence or two in the vignette and in the function documentation would help to avoid misunderstanding of vars_use. Harmony has a wide range of users, from statisticians to self-taught biologists coding in R, so I think more detail in the documentation is always better than less.
I would like to see a more precise definition of
vars_usein the software documentation. I understand that the purpose of it is to specify sources of unwanted variation (e.g. Chromium 3' versus Chromium 5'). However, a colleague of mine thinks that variables of wanted variation, such as smoker versus non-smoker, should be specified tovars_use. A clear sentence or two in the vignette and in the function documentation would help to avoid misunderstanding ofvars_use. Harmony has a wide range of users, from statisticians to self-taught biologists coding in R, so I think more detail in the documentation is always better than less.