3
To answer the first part of your question, the dependent and independent variable of X-WAS is kind of arbitrary and dependent on the question you asked. But it gradually becomes a convention in the field after the initial name and concept are accepted by the community. For example, GWAS from the very beginning is written as condition ~ SNP, and there is no ...
2
When you fit a model, you need to check whether it's overly determined, meaning some terms cannot be determined. We can look at one of your samples, for example only for RB5 and Nocardia_nova_SH22a_RB20_RB56:
df = structure(list(X = c(226L, 227L, 228L, 229L, 230L, 231L, 232L,
233L, 234L, 235L, 236L, 237L, 238L, 239L, 240L, 241L, 242L, 243L,
244L, 245L, ...
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