Information about the pipeline

[collins...@gmail.com]

Hi everyone,

I'm following the pipeline of Micca and it is pretty easy to understand. Just at the end, one of the last passage is not very clear to me:

ps.rarefied = rarefy_even_depth(ps, rngseed=1, sample.size=0.9*min(sample_sums(ps)), replace=F)

I don't understand what does it means that 0.9*min etc?

Thank you for your support

[Irene Stefanini]

hi,

in my understanding, 0.9*min(sample_sums(ps)) means that you are setting the threshold of the rarefaction to the 90% of reads you have in the sample with the lowest coverage.

with sample_sums(ps) (phyloseq package) you calculate the number of reads in each sample, then you find the lowest one (min), and finally, you calculate the 90% of that value.

I hope this can help.

best wishes