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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/
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Extract Alpha Diversity Output into excel or .csv file #1587

Open vee3capp opened 2 years ago

vee3capp commented 2 years ago

Does anyone know how to extract alpha diversity outputs from the estimate_richness () function? I am having a hard time finding the correct way to format the data. I also use the Dunn Test and want to extract the Z and p-values.

alpha.pb2<-estimate_richness(post.bloat.two) cbind.pb2 <- cbind(sample_data(post.bloat.two), alpha.pb2) dunnTest(Chao1~location, data=cbind.pb2, method="bh") -> want to extract this output

vee3capp commented 2 years ago

image This what the output looks like