Fails if slo$sample_to_covariates is a data.table

bartongroup / RATS

Relative Abundance of Transcripts: An R package for the detection of Differential Transcript isoform Usage.

MIT License

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Fails if slo$sample_to_covariates is a data.table #13

Closed alexpenson closed 7 years ago

alexpenson commented 7 years ago

Thanks for the package!

A sleuth object created with a data.table as a sample_to_covariates table leads to the following error:

Creating look-up structures...
Error in `[.data.table`(covariates, , varname) :
  j (the 2nd argument inside [...]) is a single symbol but column name 'varname' is not found. Perhaps you intended DT[,..varname] or DT[,varname,with=FALSE]. This difference to data.frame is deliberate and explained in FAQ 1.1.

This is the offending line: func.R#L196

fruce-ki commented 7 years ago

Hello Alex!

Thank you for reporting this! I was not aware it was possible for sleuth objects to have the covariates in data.table format.

Cheers!

Kimon

fruce-ki commented 7 years ago

[x] Update data emulator to create covariates in data.table format.
[x] Create unit tests
[x] Tests replicate the issue.
[x] Fix offending syntax.
[x] Pass tests.

fruce-ki commented 7 years ago

@alexpenson

Dear Alex

I just pushed a patch for the covariate parser to the current developmental version 0.3.7. Can I ask you, please, to try it with your data and let me know if it behaves as expected?

[x] Patched code behaves correctly with the data that triggered the bug.

Thanks!

Kimon

PS. Instructions for obtaining the developmental version are included in the vignettes.

alexpenson commented 7 years ago

Yes it works 👍 Thanks

fruce-ki commented 7 years ago

Awesome! I'll release the next snapshot version by the end of this month.