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benjjneb / decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
https://benjjneb.github.io/decontam/
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Better documentation of behavior for taxa present in 1 sample #1

Closed benjjneb closed 6 years ago

benjjneb commented 7 years ago

From Nicole:

I also have a request for decontam: By definition, isContaminant() only works for taxa that are found in 1+ samples. Can you add a note about that in the isContaminant() documentation? When I first ran the function, my logical vector contained lots of NAs because I hadn't yet excluded taxa found in only 1 sample. This could be confusing for some users.