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explodecomputer / tryx

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Errors when using data from local files #22

Open mardissino opened 2 years ago

mardissino commented 2 years ago

I am trying to use the package while using data from local files (imported and harmonised with TwoSampleMR). I am successfully detecting outliers (4 in total), and candidate traits associated with outliers at p < 5e-08 (189 in total). However, when I get to extracting and harmonising, I get this error message when harmonising:

Error in check_required_columns(outcome_dat, "outcome") : The following required columns are missing from outcome: SNP, id.outcome, outcome, beta.outcome, se.outcome, effect_allele.outcome, other_allele.outcome

I note that in x$output, it has successfully extracted "candidate_instruments" and "exposure_candidate" but not "candidate_outcome" and "candidate_exposure" - these two are missing from x$output. Is this because of the local origin of the data? Is there any way to get around this or does the data have to come from MR-Base strictly?

Thank you in advance,

MA

mvab commented 2 years ago

Hi @explodecomputer and @universe77 ,

I would really like to use MR-TRYX with an exposure from a local file. Is this not possible? (I get the same error as above)

Many thanks