Fix ampvis2 NA in metadata error #6213
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tools/ampvis2/macros.xml
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| @@ -49,6 +49,7 @@ echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave | |||
| ## the additional column in the ist file can the be used | |||
| ## to filter SampleIDs from select inputs | |||
| ## (check for character columns only .. since data in the column is otherwise converted to the corresponding type .. which fails) | |||
| data\$metadata[is.na(data\$metadata)] <- "NA" ##the comparison fails if NA values are present, see https://stackoverflow.com/questions/7355187/error-in-if-while-condition-missing-value-where-true-false-needed | |||
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Should we do this in the for loop?
What is data\$metadata[is.na(data\$metadata)] actually doing? Guess some subsetting. Intuitively I would have expected the negation of is.na (but its R, i.e. it might be unintuitive) .. also my question would be if we need to modify anything else in data.
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- You are right, this can be fixed outside the loop
data\$metadata[is.na(data\$metadata)]selects all cells which are NA- I think the data can be untouched, as only the metadata is changed, but if it should be changed to as string as "NA" or undefined or something - I am not sure - the user should probably be warned that the metadata will be modified
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@bernt-matthias ok from your side? |
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Yep. I enabled automerge. Can someone restart tests. I only have my mobile until end of the month. |
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Thanks @paulzierep |
nilchia
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Aug 24, 2024
* fix NA * bump version * added test and improved the fix
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If there are NA values in the metadata, the subset tool fails with:
Fixed by setting the values to "NA".
@bernt-matthias any suggestion ?