Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

prediction comments #42

Open
kasperdanielhansen opened this issue Sep 10, 2020 · 2 comments
Open

prediction comments #42

kasperdanielhansen opened this issue Sep 10, 2020 · 2 comments

Comments

@kasperdanielhansen
Copy link

kasperdanielhansen commented Sep 10, 2020

  1. The vignette says the predictor uses 5 genes, as does the paper, but this is hard to see from the code. If true, I suggest you to be more clear on this.

  2. You apply the predictor to your own training data set (I think). While useful, the call to cycle_npreg_outsample makes it a bit unclear what the requirement is for prediction. For example, should it have the same row names, have the same gene ordering etc?

@pcarbo
Copy link
Collaborator

pcarbo commented Nov 17, 2020

@jhsiao999 If I understand the vignette correctly, the example uses 101 genes to predict cell cycle, not 5. I do agree with @kasperdanielhansen it is a bit confusing because you talk about only needing 5 genes at the beginning of the vignette.

I also agree that it would be helpful if help(cycle_npreg_outsample) would give more information about the Y_test input argument. Currently it just says this:

Y_test: A ‘SingleCellExperiment’ object.

In particular, it is unclear how the Y_test input is supposed to align with the Y input to cycle_npreg_insample.

@pcarbo
Copy link
Collaborator

pcarbo commented Nov 17, 2020

@kasperdanielhansen Note there is also an example here that might help because it illustrates the use of both cycle_npreg_insample and cycle_npreg_outsample.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants