Spec
D2zAFScoreD2z computes a z-score of the inner product of kmer count vectors
D2z computes a z-score of the inner product of kmer count vectors
Extends | AFScore |
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All Extended | AFScore |
Defined in | <seqan/alignment_free.h> |
Signature |
template <>
struct AFScore<D2z>;
|
Member Function Overview
Member Variable Overview
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unsigned D2zAFScore::bgModelOrder
Order of the background model -
unsigned D2zAFScore::kmerSize
Size of the kmers -
bool D2zAFScore::verbose
true to enable verbose debug output.
Detailed Description
D2z can be used for alignment-free sequence comparison. The algorithm differs from the original implementation by the way masked sequences are handled
References
Kantorovitz, M. R.; Robinson, G. E., Sinha, S. A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics, 2007.
Member Functions Detail
AFScore::AFScore(kmerSize, bgModelOrder[, verbose]);
Constructor
Parameters
kmerSize
|
Size of kmer, unsigned. |
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bgModelOrder
|
Order of the background Markov model, unsigned. |
verbose
|
This option will report progress to standard output; bool, defaults to false. |
Data Races
Thread safety unknown!
Member Variables Detail
unsigned D2zAFScore::bgModelOrder
Order of the background model
unsigned D2zAFScore::kmerSize
Size of the kmers
bool D2zAFScore::verbose
true to enable verbose debug output.