Description Usage Arguments Details Value Author(s) References Examples
Computes the SimRank similarity (number of shared unique k-mers over the smallest number of unique k-mers.)
1 | simRank(x, k = 7)
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x |
an object of class DNAStringSet containing the sequences. |
k |
size of used k-mers. |
distSimRank()
returns 1-simRank()
.
simRank()
returns a similarity object of class "simil" (see proxy).
distSimRank()
returns a dist object.
Michael Hahsler
Santis et al, Simrank: Rapid and sensitive general-purpose k-mer search tool, BMC Ecology 2011, 11:11
1 2 3 4 5 6 7 8 9 10 11 | ### load sequences
sequences <- readDNAStringSet(system.file("examples/DNA_example.fasta",
package="rMSA"))
sequences
### compute similarity
simil <- simRank(sequences)
### use hierarchical clustering
hc <- hclust(distSimRank(sequences))
plot(hc)
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