search

joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
586 stars 186 forks source link

What is the difference between prune_samples, rarefy and rarefy_even_depth functions? #1693

Open Ecotone23 opened 1 year ago

Ecotone23 commented 1 year ago

Hello phyloseq community,

Can anyone help clear my confusion regarding some similar functions?

I would like to rarefy my samples using the sampling depth of 500 reads. Can I use either prune_samples(sample_sums(my_phyloseq_object)>500, my_phyloseq_object), or rarefy(my_phyloseq_object, 500), or rarefy_even_depth(my_phyloseq_object, sample.size=500, replace=FALSE) to achieve the same goal?

What's major difference among these functions? Thank you.

Best,

Gabriel

samd1993 commented 1 year ago

Prune samples will literally just filter out samples with less than 500 reads while rarefying will normalize all your samples to have exactly 500 reads. In my experience I use rarefy_even_depth.. not sure how rarefy is different.

Ecotone23 commented 1 year ago

Thanks! That is really helpful.