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Updated Practical 3 Processing 16S rRNA amplicon data (markdown)
authored
Jan 17, 2020
by
Ben Francis
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Practical-3-Processing-16S-rRNA-amplicon-data.md
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@@ -88,7 +88,7 @@ Don't worry about what this code is actually doing (clearly the developer knew w
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@@ -88,7 +88,7 @@ Don't worry about what this code is actually doing (clearly the developer knew w
> getN <- function(x) sum(getUniques(x))
> getN <- function(x) sum(getUniques(x))
> track <- cbind(out, sapply(dadaFs, getN), sapply(dadaRs, getN), sapply(mergers, getN),
> track <- cbind(out, sapply(dadaFs, getN), sapply(dadaRs, getN), sapply(mergers, getN),
rowSums(seqtab.nochim))
rowSums(seqtab.nochim))
> colnames(track) <- c("input", "filtered", "denoisedF", "denoisedR", "merged", "nonchim")
> colnames(track) <- c("input", "filtered", "denoisedF", "denoisedR", "merged", "nonchim")
> rownames(track) <- sample.names
> rownames(track) <- sample.names
> head(track)
> head(track)
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