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XiaoyangSu / AccuCor

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Additional fields added in newer El-Maven versions are interpreted as samples #23

Closed lparsons closed 2 years ago

lparsons commented 3 years ago

Newer versions of El-Maven have added new columns (namely adductName and Max Peak) which AccuCor incorrectly interprets as sample columns. These should be ignored.

One thought is to get attempt to get the column index for the last known "non-sample" column and treat all columns before that as non-sample columns. This would help AccuCor handle new columns in the future as long as there weren't added right before the sample. In this case, Max Peak seems to be right before the samples, so it wouldn't have helped there, but would have been able to handle the adductName column.

lparsons commented 3 years ago

Looking further, I believe that the adductName is the only new column added by El-Maven, while the Max Peak was likely added by a researcher manually before running AccuCor. We'll use the test_TargetedGroupReport.csv file from the El-Maven repository as a test.

lparsons commented 3 years ago

The test files from the El-Maven repository do not have isotope labeled data, thus we'll need to use our own test data instead.