inst/doc/vignette.R

In odseq: Outlier detection in multiple sequence alignments

## ---- message=FALSE-----------------------------------------------------------
set.seed(93)
library(odseq)
data("seqs")

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library(msa)
alig <- msa(seqs)

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ground_values <- c(rep(FALSE, 211), rep(TRUE, 100))
outliers <- odseq(alig, distance_metric = "affine", B = 1000)

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mean(outliers == ground_values)

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library(kebabs)
sp <- spectrumKernel(k = 3)
mat <- getKernelMatrix(sp, seqs)

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outliers_unaligned <- odseq_unaligned(mat, B = 1000, type = "similarity")

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mean(outliers_unaligned == ground_values)