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tobiasgf / lulu

r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)
GNU Lesser General Public License v3.0
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empty curated table fix #1

Open jack1120 opened 6 years ago

jack1120 commented 6 years ago

Hi Tobias,

I ran LULU as described in E_LULU_processing.RMD and got back empty _luluprocessed tables. I could see that the proc_min list (produced at line 87) was not empty, so thought that there may just be an issue with extracting the curated table. Indeed, I think I found what the issue is.

In line 88 of E_LULU_processing.RMD it reads: curated_table <- proc_min$curated_OTU_table ## extracting the curated table

However, line 179 of the Functions.R script for LULU reads: result <- list(curated_table = curation_table,

I changed line 88 of E_LULU_processing.RMD to: curated_table <- proc_min$curated_table ## extracting the curated table

This produced an OTU table that has a smaller file size and contains fewer reads than the original OTU table, so I assume that this solved the problem. Does that seem correct to you?

Thanks, Lauren

tobiasgf commented 6 years ago

Oh, yes.

That is because the documentation file for the LULU manuscript was finished before the final version of the LULU algorithm. I must have changed some names. I should correct those names in the documentation files, to keep reproducibility :-)

Thanks!