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genophenoenvo / terraref-datasets

Repository for code and small datasets derived from the TERRA REF program
MIT License
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Create file with aggregated phenotype data #24

Closed kshefchek closed 4 years ago

kshefchek commented 4 years ago

In order to perform that gwas analysis we need all relevant phenotype data in a file. Since I'm unsure of the final format, the tall format should work fine and I can convert it as needed.

MagicMilly commented 4 years ago

@kshefchek I shared the tall format trait table with you on CyVerse as a collaborator. Let me know if you aren't able to access it. I haven't done much with it since we aren't sure exactly what you need yet. The main issue is that some traits are measured multiple times in a day and sometimes divided into east and west subplots. If you need something like only one averaged value per day per plot, let me know.

If needed, the trait-ontology mappings can be found on the Google Drive for now.

kshefchek commented 4 years ago

thanks! I'll take a pass at using this file in the gwas file. In terms of measured values, I'll have to defer to someone who has domain knowledge in this area or has a better sense of the analysis goals.

MagicMilly commented 4 years ago

Closing and creating new issue #26 for traits associated with E and W subplots and / or with duplicate timestamps