isNotContaminant example in reference manual

[ScaonE]

Dear all,

In the reference manual, the isNotContaminant function is documented with one example: isNotContaminant(st, samdf$quant_reading, threshold=0.05)

Which I read as: seqtab = st neg = samdf$quant_reading threshold = 0.05

I don't understand the neg argument value. It seems like DNA quantitation data, aimed at the frequency-based method. But isNotContaminant is using the prevalence-based method and should recieve information about negative controls, e.g. samdf$Sample_or_Control, right ?

[benjjneb]

Thanks for the report, looks like a bug in the example to me!

[Xiao-lin-Liu]

I noticed this as well, and how to use it properly as I do have some seq data from low biomass samples