dgrun
commented
6 years ago Dear Robrecht,
I don't think it is a good idea to include FateID into the trajectory benchmarking, since it is not designed for the inference of complex trajectories. The goal of this method is a probabilistic quantification of fate bias. Although the package offers limited support for trajectory inference by principal curve fitting in a dimensional reduction representation it is not designed for resolving complex technologies. I will work on methods in the future for exploiting fate bias in a more sophisticated way for the purpose of trajectory inference.
A current shortcoming is, that trajectories are derived by this rather simple procedure in a dimensional reduction representation. In the future I will try to include the FateID probabilities as prior information into the StemID analysis. This would then be more appropriate for benchmarking...
I saw you also included STEMNET which has a very similar objective to FateID. Do you test the two method in the same way as all other methods, or are they subject to separate benchmaking?
Thanks!
Best wishes, Dominic
On Fri, Jun 29, 2018 at 3:11 PM, Robrecht Cannoodt <notifications@github.com
wrote:
Hello @dgrun https://github.com/dgrun
This issue is for discussing the wrapper for your trajectory inference method, FateID, which we wrapped for our benchmarking study ( 10.1101/276907 https://doi.org/10.1101/276907). In our dynmethods https://github.com/dynverse/dynmethods framework, we collected some meta information about your method, and created a docker wrapper so that all methods can be easily run and compared. The code for this wrapper is located in a docker container https://github.com/dynverse/dynmethods/tree/master/containers/fateid. The way this container is structured is described in this vignette https://dynverse.github.io/dynwrap/articles/create_ti_method_docker.html .
We are creating this issue to ensure your method is being evaluated in the way it was designed for. The checklist below contains some important questions for you to have a look at.
[] Parameters, defined in definition.yml https://github.com/dynverse/dynmethods/tree/master/containers/fateid/definition.yml (more info https://dynverse.github.io/dynwrap/articles/create_ti_method_docker.html#parameters)
- Are all important parameters described in this file?
- For each parameter, is the proposed default value reasonable?
- For each parameter, is the proposed parameter space reasonable (e.g. lower and upper boundaries)?
- Is the description of the parameters correct and up-to-date?
[] Input, defined in definition.yml https://github.com/dynverse/dynmethods/tree/master/containers/fateid/definition.yml and loaded in run.R https://github.com/dynverse/dynmethods/tree/master/containers/fateid/run.R (more info https://dynverse.github.io/dynwrap/articles/create_ti_method_docker.html#input)
- Is the correct type of expression requested (raw counts or normalised expression)?
- Is all prior information (required or optional) requested?
- Would some other type of prior information help the method?
[] Output, defined in definition.yml https://github.com/dynverse/dynmethods/tree/master/containers/fateid/definition.yml and saved in run.R https://github.com/dynverse/dynmethods/tree/master/containers/fateid/run.R (more info https://dynverse.github.io/dynwrap/articles/create_ti_method_docker.html#output)
- Is the output correctly processed towards the common trajectory model https://github.com/dynverse/dynwrap#dynwrap? Would some other postprocessing method make more sense?
- Is all relevant output saved (dimensionality reduction, clustering/grouping, pseudotime, ...)
[] Wrapper script, see run.R https://github.com/dynverse/dynmethods/tree/master/containers/fateid/run.R (more info https://dynverse.github.io/dynwrap/articles/create_ti_method_docker.html#doing-trajectory-inference)
- This is a script that is executed upon starting the docker container. It will receive several input files as defined by definition.yml, and is expected to produce certain output files, also as defined by definition.yml.
- Is the script a correct representation of the general workflow a user is expected to follow when they want to apply your method to their data?
- [] Quality control, see the qc worksheet https://docs.google.com/spreadsheets/d/1GWWdndfTPtXPsCXK07jU03MmhIJHmv28E7YiMnQ_0Xo//edit#gid=271451895
- We also evaluated the implementation of a method based on a large check list of good software software development practices.
- Are the answers we wrote down for your method correct and up to date? Do you disagree with certain answers? (Feel free to leave a comment in the worksheet)
- You can improve the QC score of your method by implementing the required changes and letting us know. Do not gloss over this, as it is the easiest way to improve the overall ranking of your TI method in our study!
The most convenient way for you to test and adapt the wrapper is to install dyno https://github.com/dynverse/dyno, download and modify these files https://github.com/dynverse/dynmethods/tree/master/containers/fateid, and run your method on a dataset of interest or one of our synthetic toy datasets. This is further described in this vignette https://dynverse.github.io/dynwrap/articles/create_ti_method_docker.html. Once finished, we prefer that you fork the dynmethods repository https://github.com/dynverse/dynmethods, make the necessary changes, and send us a pull request. Alternatively, you can also send us the files and we will make the necessary changes.
If you have any further questions or remarks, feel free to reply to this issue.
Kind regards, @zouter https://github.com/zouter and @rcannood https://github.com/rcannood
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dynverse/dynmethods/issues/81, or mute the thread https://github.com/notifications/unsubscribe-auth/AKo-9KFsF_tIFAYxpf5kFfi9xr1xlXp4ks5uBiefgaJpZM4U86KF .
rcannood
Hello @dgrun
This issue is for discussing the wrapper for your trajectory inference method, FateID, which we wrapped for our benchmarking study (10.1101/276907). In our dynmethods framework, we collected some meta information about your method, and created a docker wrapper so that all methods can be easily run and compared. The code for this wrapper is located in a docker container. The way this container is structured is described in this vignette.
We are creating this issue to ensure your method is being evaluated in the way it was designed for. The checklist below contains some important questions for you to have a look at.
definition.yml, and is expected to produce certain output files, also as defined bydefinition.yml.The most convenient way for you to test and adapt the wrapper is to install dyno, download and modify these files, and run your method on a dataset of interest or one of our synthetic toy datasets. This is further described in this vignette. Once finished, we prefer that you fork the dynmethods repository, make the necessary changes, and send us a pull request. Alternatively, you can also send us the files and we will make the necessary changes.
If you have any further questions or remarks, feel free to reply to this issue.
Kind regards, @rcannood and @zouter