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Updated Practical 3 Processing 16S rRNA amplicon data (markdown) authored by Ben Francis's avatar Ben Francis
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Practical-3-Processing-16S-rRNA-amplicon-data.md
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...@@ -115,6 +115,7 @@ Like I said at the beginning, installation of DADA2 wasn't easy, and so in this ...@@ -115,6 +115,7 @@ Like I said at the beginning, installation of DADA2 wasn't easy, and so in this
seqtab <- data.frame(seqtab) seqtab <- data.frame(seqtab)
colnames(seqtab) <- paste(taxtable[, 1], taxtable[, 2], taxtable[, 3], taxtable[, 4], colnames(seqtab) <- paste(taxtable[, 1], taxtable[, 2], taxtable[, 3], taxtable[, 4],
taxtable[, 5], taxtable[, 6], as.character(1:length(taxtable[, 1])), sep="-") taxtable[, 5], taxtable[, 6], as.character(1:length(taxtable[, 1])), sep="-")
seqtab[, grep("Chloroplast|Mitochondria", colnames(seqtab), invert=TRUE)]
seqtab <- seqtab/rowSums(seqtab) seqtab <- seqtab/rowSums(seqtab)
seqtab <- seqtab[, sapply(seqtab, function(x) max(x)) >= min_abund] seqtab <- seqtab[, sapply(seqtab, function(x) max(x)) >= min_abund]
seqtab$sample <- rownames(seqtab) seqtab$sample <- rownames(seqtab)
......