Cannot run cis.map_independent

[idinsmore1]

Cannot run cis.map_independent

[francois-a]

Hi, this error is currently raised when cis_df contains no phenotypes with q-value ≤ 0.05 (default). I added a more explicit error in c41d546.

[idinsmore1]

@francois-a Thanks for getting back to me, but this is not true. From the above output, I'm also getting the following log

cis-QTL mapping: conditionally independent variants
  * 2225 samples
  * 4858/5000 significant phenotypes
  * 71 covariates
  * 3130722 variants

And, when looking at qvalues directly, I can confirm this is true. What's strange is that if I run map_independent directly on the object returned from map_cis, it runs. However, if I save the output of map_cis to a file, then read in the dataset from the file, it no longer works.

[francois-a]

It sounds like an issue with writing/reading the file then? Can you please post a reproducible example?

[idinsmore1]

I played around with the files a little bit, it seems that by setting the phenotype_id to be the index, things seem to running now. Is it possible to filter the snps that you want to test for conditional independence? I have ~3 million snps in my genetic set, but I'm particularly interested in about 300 of them. Can I filter down my results from cis.map_cis to only test the independence of those 300? Thanks for your help!