Updated Practical 3 Processing 16S rRNA amplicon data (markdown) authored by Ben Francis's avatar Ben Francis
...@@ -88,7 +88,7 @@ Don't worry about what this code is actually doing (clearly the developer knew w ...@@ -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)
... ...
......