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"),[
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