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java.lang.Objectedu.cmu.cs.sb.core.DataSetCore
edu.cmu.cs.sb.stem.STEM_DataSet
public class STEM_DataSet
Class implementing clustering methods implemented in STEM
Nested Class Summary | |
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static class |
STEM_DataSet.ProfileRec
Class implements a record for a profile, storing its ID, the number of genes assigned, the number of genes expected, and the uncorrected p-value of the number of genes assigned versus expected |
static class |
STEM_DataSet.Profilerecdistcomparator
Compares two profiles records based on their dprofiledist variable |
Field Summary | |
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static int |
ALLPERMSTHRESH
|
static double |
DSAME
|
static double |
FLOATERROR
|
double[][] |
profileavg
The first index is the profile, the second index is the time point. |
double[][] |
profilestd
The first index is the profile, the second index is the time point. |
double[][] |
profilesumsq
The first index is the profile, the second index is the time point. |
Fields inherited from class edu.cmu.cs.sb.core.DataSetCore |
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badd0, bfullrepeat, bmaxminval, bspotincluded, btakelog, data, dmincorrelation, dsamplemins, dthresholdvalue, genenames, generepeatspottimedata, generepeatspottimepma, genespottimedata, genespottimepma, htFiltered, nmaxmissing, numcols, numrows, otherInputFiles, pmavalues, probenames, sortedcorrvals, szGeneHeader, szInputFile, szProbeHeader |
Constructor Summary | |
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STEM_DataSet(DataSetCore theDataSetCore,
STEM_DataSet theSTEM_DataSet)
Constructor that simply copies all fields in theDataSetCore and theSTEM_DataSet |
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STEM_DataSet(java.lang.String szInputFile,
int nmaxmissing,
double dminclustdist,
double dthresholdvalue,
double dmincorrelation,
double dalphaval,
double dpercentileclust,
int nmaxchange,
int nmaxprofiles,
double dmaxcorrmodel,
int nsamplesgene,
long nsamplesmodel,
double[][] modelprofiles,
int nfdr,
boolean btakelog,
boolean bspotincluded,
boolean brepeatset,
boolean badd0,
boolean bmaxminval,
boolean ballpermuteval,
boolean bfullrepeat)
Constructor for a STEM method clustering |
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STEM_DataSet(java.lang.String szInputFile,
int nmaxmissing,
double dthresholdvalue,
double dmincorrelation,
int nmaxprofiles,
int nmaxchange,
boolean btakelog,
boolean bspotincluded,
boolean brepeatset,
boolean badd0,
boolean bmaxminval,
boolean bfullrepeat)
Constructor for k-means clustering |
Method Summary | |
---|---|
void |
assignall0()
Sets all genes to be assigned to profile index 0 |
boolean |
closeToAllNeighbors(STEM_DataSet.ProfileRec insertProfile,
java.util.TreeSet tsNeighborhood)
Returns true iff neighborProfile correlation with all profiles in tsNeighborhood is greater than or equal to dminclustdist |
void |
clusterprofiles(boolean[] significant,
java.util.ArrayList clustersofprofiles,
boolean bnormal)
Method for clustering profiles |
void |
compactprofiles2(double dmaxcorrelationprofiles,
int nmaxprofiles)
Implements the greedy algorithm to select a subset of the candidate model profiles based on dmaxcorrelationprofiles and nmaxprofiles |
void |
computeaveragetally()
Computes the expected number of genes assigned to a profile based on a permutation test of time points |
void |
computeprofilestats()
Computes the average and standard deviation of the expression values of genes assigned to the same profile |
void |
computePvaluesAssignments()
Computes the p-value for genes assigned to the same profile |
void |
findbestgroupassignments()
Finds the best profile which matches each gene |
void |
kmeans()
Implements the k-means clustering method |
void |
modelprofilestats(double[] dsumy,
double[] dsumysq,
double[] dsqrty)
Computes sum and variance statistics on model profiles |
void |
tallyassignments()
Counts the number of genes assigned to each profile |
Methods inherited from class edu.cmu.cs.sb.core.DataSetCore |
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addExtraToFilter, averageAndFilterDuplicates, dataSetReader, filterdistprofiles, filterDuplicates, filtergenesgeneral, filtergenesthreshold1point, filtergenesthreshold2, filterMissing, filterMissing1point, logratio2, mergeDataSets |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static double DSAME
public static double FLOATERROR
public static int ALLPERMSTHRESH
public double[][] profileavg
public double[][] profilestd
public double[][] profilesumsq
Constructor Detail |
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public STEM_DataSet(DataSetCore theDataSetCore, STEM_DataSet theSTEM_DataSet)
public STEM_DataSet(java.lang.String szInputFile, int nmaxmissing, double dthresholdvalue, double dmincorrelation, int nmaxprofiles, int nmaxchange, boolean btakelog, boolean bspotincluded, boolean brepeatset, boolean badd0, boolean bmaxminval, boolean bfullrepeat) throws java.io.IOException, java.io.FileNotFoundException, java.lang.IllegalArgumentException
java.io.IOException
java.io.FileNotFoundException
java.lang.IllegalArgumentException
public STEM_DataSet(java.lang.String szInputFile, int nmaxmissing, double dminclustdist, double dthresholdvalue, double dmincorrelation, double dalphaval, double dpercentileclust, int nmaxchange, int nmaxprofiles, double dmaxcorrmodel, int nsamplesgene, long nsamplesmodel, double[][] modelprofiles, int nfdr, boolean btakelog, boolean bspotincluded, boolean brepeatset, boolean badd0, boolean bmaxminval, boolean ballpermuteval, boolean bfullrepeat) throws java.io.IOException, java.io.FileNotFoundException, java.lang.IllegalArgumentException
java.io.IOException
java.io.FileNotFoundException
java.lang.IllegalArgumentException
Method Detail |
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public void tallyassignments()
public void computeprofilestats()
public void computePvaluesAssignments()
public void kmeans()
public boolean closeToAllNeighbors(STEM_DataSet.ProfileRec insertProfile, java.util.TreeSet tsNeighborhood)
public void clusterprofiles(boolean[] significant, java.util.ArrayList clustersofprofiles, boolean bnormal) throws java.lang.Exception
java.lang.Exception
public void computeaveragetally()
public void assignall0()
public void modelprofilestats(double[] dsumy, double[] dsumysq, double[] dsqrty)
public void compactprofiles2(double dmaxcorrelationprofiles, int nmaxprofiles)
public void findbestgroupassignments()
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