Spec
N2 AFScoreN2 computes the inner product of the standardised neighbourhood kmer count vectors.
N2 computes the inner product of the standardised neighbourhood kmer count vectors.
Extends | AFScore |
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All Extended | AFScore |
Defined in | <seqan/alignment_free.h> |
Signature |
template <>
struct AFScore<N2>;
|
Member Function Overview
Member Variable Overview
-
unsigned N2AFScore::bgModelOrder
Order of the background model -
unsigned N2AFScore::kmerSize
Size of the kmers. -
unsigned N2AFScore::mismatches
Approximate word matches [0(exact)/1(one mismatch)] -
double N2AFScore::mismatchWeight
Weight for approximate word matches -
CharString N2AFScore::outputFile
When specified, all kmerWeights for every sequence will be written to this file. -
CharString N2AFScore::revCom
Scoring of reverse complements words, CharString [''/'max'/'min'/'mean'/'both_strands'/]. -
bool N2AFScore::verbose
true to enable verbose debug output.
Detailed Description
N2 can be used for alignment-free sequence comparison.
References
Jonathan Goeke, Marcel H. Schulz, Julia Lasserre, and Martin Vingron. timation of Pairwise Sequence Similarity of Mammalian Enhancers with Word Neighbourhood Counts. Bioinformatics 012).
Member Functions Detail
AFScore::AFScore(kmerSize, bgModelOrder, outputFile, verbose);
AFScore::AFScore(kmerSize, bgModelOrder, revCom, outputFile, verbose);
AFScore::AFScore(kmerSize, bgModelOrder, revCom, mismatches, mismatchWeight, outputFile, verbose);
Constructor
Parameters
kmerSize
|
Size of kmer, unsigned. |
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bgModelOrder
|
Order of the background Markov model, unsigned. |
outputFile
|
When specified, all normalised and standardised kmer neighbourhood counts will be written to this file for every sequence, CharString. |
revCom
|
Scoring of reverse complements words [''/'max'/'min'/'mean'/'both_strands'/], CharString. |
verbose
|
This option will report progress to standard output, bool, defaults to false. |
mismatches
|
Includes words with one mismatch into the word neighbourhood, unsigned, 0 or 1. |
mismatchWeight
|
Weight of word counts with one mismatch, double. |
Data Races
Thread safety unknown!
See Also
Member Variables Detail
unsigned N2AFScore::bgModelOrder
Order of the background model
unsigned N2AFScore::kmerSize
Size of the kmers.
unsigned N2AFScore::mismatches
Approximate word matches [0(exact)/1(one mismatch)]
double N2AFScore::mismatchWeight
Weight for approximate word matches
CharString N2AFScore::outputFile
When specified, all kmerWeights for every sequence will be written to this file.
CharString N2AFScore::revCom
Scoring of reverse complements words, CharString [''/'max'/'min'/'mean'/'both_strands'/].
bool N2AFScore::verbose
true to enable verbose debug output.