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waldronlab / lefser

R implementation of the LEfSe method
https://waldronlab.io/lefser/
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Specify the datataset you want to use #3

Closed lwaldron closed 4 years ago

lwaldron commented 4 years ago

It will be clearer to specify the dataset you want, rather than using wildcards then [[8]] which add unnecessary complexity:

https://github.com/waldronlab/lefser/blob/ad7a229b02d1c947e7910e31efe5bd8b424d4f0c/vignettes/lefser.Rmd#L45

lwaldron commented 4 years ago

The currently selected dataset [[8]] can be retrieved as follows:

dataset <- curatedMetagenomicData("DhakanDB_2019.metaphlan_bugs_list.stool", counts=TRUE, dryrun = FALSE)[[1]]

But the DhakanDB_2019 dataset is all controls and doesn't contain any adenoma patients. From the numerical argument [[8]] I'm not sure which dataset you wanted, and the order of datasets isn't guaranteed to remain constant with cMD updates. The above command downloads all 50-some metaphlan_bugs_list.stool datasets in cMD then selects one, so a great efficiency improvement will also be realized by just downloading the one dataset you want.

lwaldron commented 4 years ago

Solved in 15a6c93