conditionally and persisitently rare taxa #98
+101
−0
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
Signed-off-by: Daena Rys <[email protected]>
TuomasBorman
requested changes
Nov 14, 2024
Comment on lines
+54
to
+77
| # Calculate metrics for each split subject/group | ||
| results_list <- lapply(split_data, function(sub_data) { | ||
| # Initialize a list to hold results for each metric | ||
| metric_results <- list() | ||
|
|
||
| # Loop through each metric and calculate it | ||
| for (metric in metrics) { | ||
| # Check if the metric is supported and calculate accordingly | ||
| if (metric == "CRT") { | ||
| crt_results <- .calculateCRT(sub_data, thresholds[["CRT"]]) | ||
| metric_results[["CRT"]] <- crt_results | ||
| } else { | ||
| stop(paste("Metric", metric, "is not supported yet."), | ||
| call. = FALSE) | ||
| } | ||
| } | ||
|
|
||
| # Add the calculated metrics to the metadata (colData or rowData) | ||
| for (metric in names(metric_results)) { | ||
| colData(sub_data)[[metric]] <- metric_results[[metric]] | ||
| } | ||
|
|
||
| return(sub_data) | ||
| }) |
There was a problem hiding this comment.
It would be more efficient to:
- Get matrix
- Get the list which has vectors as elements. Each vector represent members of each group
- Loop through this list
- Select the group members from the matrix
- Calculate values
- Combine all the results and sort values based on sample names
- Add to colData (in add* method)
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Outdated suggestions cannot be applied.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.
ping #83