The bioBakery help forum

How halla handles missing data


I would like to ask how halla deals with missing data. I saw in previous versions the argument “MISSING_CHAR” but it’s no longer in the help message from the current version.


HAllA uses pandas.read_table to read in the data, so it detects missing values using that. You can scroll down to na_values to see the strings that get detected as NAs. HAllA also adds empty cells to that list.

When evaluating associations, NAs are dropped.

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