Bug fixes for concurrent errors from special characters in inferGRN formulas #74
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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
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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.