Bug fixes for concurrent errors from special characters in inferGRN formulas#74
Open
mbrovkin wants to merge 16 commits intoquadbio:mainfrom
Open
Bug fixes for concurrent errors from special characters in inferGRN formulas#74mbrovkin wants to merge 16 commits intoquadbio:mainfrom
mbrovkin wants to merge 16 commits intoquadbio:mainfrom
Conversation
added functionality to escape special characters within gene names
fix attempt quadbio#2 for the special characters non-functionality
escape problematic characters in the formula accession
Update handling for special characters in gene names
fixed line from object@meta.data to object@data@meta.data
backtick peaks
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
There were several issues noted coming from chromosome names and gene names containing special characters. For example, in the dm6 assembly, the NCBI chromosome notations are 3R, 3L, etc, throwing the formula input. Gene name problems included those starting with integers, containing parentheses, colons, and the gene "if" which was parsed as an if/then statement - to say the least.
I have updated the code to account for that by automatically backticking regions and gene names and then removing those backticks in the code. This should also remove the necessity for str_replace_all to convert "-" to "_", though I have not removed these lines. This should be a universal fix, but please let me know if it is not.