Hierarchical timepoints #2
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Go from collapsed_sequence_counts.tsv to annotated_sequence_counts.tsv. This converts location of "USA" to "USA_2023-24", etc... by appending timepoint
If "other" is the same label across timepoints, estimating a single fitness for "other" will be wonky
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Instead of "scaffolding" across independently run timepoints, instead run a hierarchical model where each timepoint is its own "location", ie
It should be okay that variants don't fully span locations (aka timepoints) in the hierarchical model as long as there is a pivot bridge between locations.
This combines sequence counts from different timepoints into a single aggregated sequence count file. In this aggregation, the "location" field is suffixed by timepoint. Hierarchical MLR is run on the aggregated timepoints.