@valentynbez created a PR https://github.com/qiime2/q2-composition/pull/82 which supports this feature, however we really want to create a new flag, such as: filter_missing: bool = False which, when true, would not raise an error when samples have missing values in their metadata, instead filtering them out.
As @valentynbez mentions:
During the analysis, I had some missing metadata values. To counter it I had to:
revert to a feature-table step
filter it, filter than collapse it
add_pseudocount
filter metadata
finally run ancom
Missing values in metadata are human-introduced errors, they appear quite often. This is an inconvenient workflow for the user.
General behavior and tests are already written in the above PR, we just need to adapt it to use a flag instead of always filtering.
(Please rebase the commit history such that it includes their commit(s) if you adapt the above PR, that way @valentynbez get's proper attribution.)
@valentynbez created a PR https://github.com/qiime2/q2-composition/pull/82 which supports this feature, however we really want to create a new flag, such as:
filter_missing: bool = Falsewhich, when true, would not raise an error when samples have missing values in their metadata, instead filtering them out.As @valentynbez mentions:
General behavior and tests are already written in the above PR, we just need to adapt it to use a flag instead of always filtering. (Please rebase the commit history such that it includes their commit(s) if you adapt the above PR, that way @valentynbez get's proper attribution.)