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…g results[[molecular_id]][["variant_names"]] structure issue
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harmonize_twas() function:
In the
harmonize_twas()function, the 4th column inld_info_datacorresponds toX4, notV4. To avoid the column name error, I have used the 4th column directly (ld_info_data[, 4]) instead of referencing the column name.For the other fix, if the filtered data is empty, I don’t want the process to stop. Instead, I have implemented logic to skip the current context and move on to the next one.
In
misc.R, if all p-values areNA, I made sure that qvalueNAis returned in such cases, avoiding errors.