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snystrom / memes

An R interface to the MEME Suite
https://snystrom.github.io/memes/
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flyFactorSurvey_cleaned.meme throws duplicated ID warnings in runTomTom #78

Closed snystrom closed 3 years ago

snystrom commented 3 years ago

This file should have all unique entries so this shouldn't happen. Unless tomtom can Identify that the matrices are identical and it's saying they're duplicate ID also...

Double check this & make sure flyFactorSurvey_cleaned.meme is generated properly such that no non-unique motifs are present.

If it's true that TomTom recognizes identical matrices in addition to similar metadata, then add this examination to tidy_motifs.Rmd using a pearson correlation from universalmotif to remove all duplicate entries (ie where R = 1).

snystrom commented 3 years ago

Add deduplicate_motifs function? Maybe that's universalmotif purview.

snystrom commented 3 years ago

ex.

grep -A 15 Fer flyFactorSurvey_cleaned.meme grep -A 15 HLH54F_da_SANGER_5 flyFactorSurvey_cleaned.meme

will show some of these issues.

snystrom commented 3 years ago

Addressed in 60171d1. where I develop more cleaning methods for FlyFactor.