Function
getKmerSimilarityMatrix
Creates a matrix storing the number of common q-grams between all pairs of sequences.
getKmerSimilarityMatrix(index, distMat[, seqSet])
Include Headers
seqan/index.h
Parameters
index
A q-gram index.
Types: IndexQGram
distMat
The resulting q-gram similarity matrix.
seqSet
Contains sequence numbers if only a subset of sequences should be compared.
Remarks
distMat need to be a container of a floating point type and will be resized to seqCount*seqCount, where seqCount is the number of sequences in the index/in seqSet. The fraction of common q-grams between sequence i and j is stored at position i*seqCount + j. It sums up the minimum number of q-gram occurrences between both sequences for each q-gram and normalizes it.
Member of
SeqAn - Sequence Analysis Library - www.seqan.de
 

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