Merged
Conversation
1. In LD.R, exchange `arrange` and `check order`. This is the same logic in the previous code, otherwise, we need to input an ordered `ld_meta_file`. - Met an error. 2. In raiss.R, if sumstat does not contain known varaints (raiss_single_matrix.R), it return NULL. we can not check `nrow`. - Met an error.
Contributor
okay i caught this when i was working on the code yesterday thinking that if we "arrange" it already then the consecutive check would not make sense. Maybe this function is not that useful after all anyways and it is cleaner we remove that check. |
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
arrangeandcheck order. This is the same logic in the previous code, otherwise, we need to input an orderedld_meta_file. - Met an error in all genes, since our ld_meta_file is not ordered by chr and pos.nrow. - Met an error in chr1_ENSG00000143418 and chr1_ENSG00000143437 in Kunkle sumstat. Kunkle does not have variants in the first LD block, then it reported an errorError in if (nrow(combined_result) == 0) { : argument is of length zero.