vignettes/intro.R

In larssnip/microclass: Tools for taxonomic classification of prokaryotes

## ----message=FALSE------------------------------------------------------------
library(microclass)
KmerCount("ATGCCTGAACTGACCTGC", K = 1, col.names = TRUE)
KmerCount("ATGCCTGAACTGACCTGC", K = 2, col.names = TRUE)
KmerCount("ATGCCTGAACTGACCTGC", K = 3, col.names = TRUE)

## ---- eval=F------------------------------------------------------------------
#  library(microcontax)
#  data(small.16S)
#  tax.tab <- taxMachine(small.16S$Sequence)
#  head(tax.tab)

## ---- eval=F------------------------------------------------------------------
#  genus <- sapply(strsplit(small.16S$Header,split=" "),function(x){x[2]})
#  cat("Number of errors:", sum(genus != tax.tab$Genus))

## ---- fig.cap = "Classification uncertainty scores", eval=F-------------------
#  par(mfrow = c(1,2), mar = c(2.5,2,3,1))
#  boxplot(tax.tab$D.score, factor(genus), main = "D-score")
#  boxplot(tax.tab$R.score, factor(genus), main = "R-score")

## ---- eval=F------------------------------------------------------------------
#  tax.tab$Is.Recognized <- tax.tab$P.recognized>0.01
#  tax.tab[35:45,]

## ---- eval=F------------------------------------------------------------------
#  rdp <- rdpTrain(small.16S$Sequence[seq(1,71,2)], genus[seq(1,71,2)])  # training step
#  predicted <- rdpClassify(small.16S$Sequence[seq(2,71,2)], rdp)        # classification step
#  cat( "Number of errors:", sum(predicted != genus[seq(2,71,2)]) )