Construct a phyloseq object directly from the dada2 outputs
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Manijeh • 0
Last seen 8 weeks ago

I have a group of samples, 8 of them control, and the rest have a disease. we want to analyze their microbiome in these two groups. I can do the analysis in DADA2 and I got response from ASSIGN TAXONOMY. But for the phyloseq section, I cant define "ps" or "phyloseq object" for further analysis. I don't know what should I replace instead of these commands in the tutorial.

``samples.out <- rownames(seqtab.nochim) subject <- sapply(strsplit(samples.out, "D"),[, 1) gender <- substr(subject,1,1) subject <- substr(subject,2,999) day <- as.integer(sapply(strsplit(samples.out, "D"),[`, 2)) samdf <- data.frame(Subject=subject, Gender=gender, Day=day) samdf$When <- "Early" samdf$When[samdf$Day>100] <- "Late" rownames(samdf) <- samples.out


phyloseq dada2 • 93 views

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