public class DeBruijnMotifComparison extends Object
Constructor and Description |
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DeBruijnMotifComparison() |
Modifier and Type | Method and Description |
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static Pair<Integer,Double> |
compare(double[] profile1,
double[] profile2,
int maxShift)
Computes the correlation of the two score profiles with relative shifts of the profiles of up to
maxShift . |
static Pair<double[][],int[][]> |
getClusterRepresentative(ClusterTree<StatisticalModel> tree,
int n)
Returns a position weight matrix (PWM) representation of the root node of the given cluster tree and
also computed the relative shifts of the motifs such that they align best with the consensus motif at the root.
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static double[][] |
getProfilesForMotif(CyclicSequenceAdaptor[] ad,
StatisticalModel model,
boolean revcom,
boolean exp)
Returns the score profile on a De Bruin sequence for a De Bruijn sequence.
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static double[][] |
getProfilesForMotif(StatisticalModel model,
int n,
boolean revcom,
boolean exp)
Returns the score profile on a De Bruin sequence for a De Bruijn sequence.
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public static Pair<Integer,Double> compare(double[] profile1, double[] profile2, int maxShift)
maxShift
.profile1
- the first profileprofile2
- the second profilemaxShift
- the maximum relative shiftpublic static double[][] getProfilesForMotif(StatisticalModel model, int n, boolean revcom, boolean exp) throws Exception
model
- the modeln
- the length of n-mers represented in the De Bruijn sequencerevcom
- if the reverse complementary profile should be computedexp
- if the exponential scores should be returnedException
- if the score could not be computedpublic static double[][] getProfilesForMotif(CyclicSequenceAdaptor[] ad, StatisticalModel model, boolean revcom, boolean exp) throws Exception
model
- the modelad
- the cyclic sequence(s) for which the score profile(s) should be computedrevcom
- if the reverse complementary profile should be computedexp
- if the exponential scores should be returnedException
- if the score could not be computedpublic static Pair<double[][],int[][]> getClusterRepresentative(ClusterTree<StatisticalModel> tree, int n) throws Exception
tree
- the tree of motifsn
- the length of n-mers used for the De Bruijn sequence for determining shiftsException
- if the score could not be computed