edu.cmu.cs.sb.stem
Class STEM_GoAnnotations
java.lang.Object
edu.cmu.cs.sb.core.GoAnnotations
edu.cmu.cs.sb.stem.STEM_GoAnnotations
public class STEM_GoAnnotations
- extends GoAnnotations
Extends GoAnnotations with methods specific to STEM for analyzing GoAnnotations
Fields inherited from class edu.cmu.cs.sb.core.GoAnnotations |
algoAll, algoAllbase, bactual, bcluster, bcontoval, bfontoval, bpontoval, brandomgoval, extragenes, extraprobes, goAll, htAlt, htAncestors, htFullCount, htGeneNames, htGO, htGoLabels, htIDCategory, nGeneSet, nlegalgo, nmaxsize, nmingo, nmingolevel, nsamplespval, numcategory, numtotalgenes, szcategoryIDval, szevidenceval, szextraval, szGoCategoryFile, szGoFile, szorganismsourceval, szSelectedGO, szsortcommand, sztaxonval, szxrefsourceval, szxrefval, theClusterRecIDpval, theRecIDpval, tpgr |
Constructor Summary |
STEM_GoAnnotations(java.lang.String szorganismsourceval,
java.lang.String szxrefsourceval,
java.lang.String szxrefval,
java.lang.String szGoFile,
java.lang.String szGoCategoryFile,
java.lang.String[] baseGenes1,
java.lang.String[] baseProbes1,
int nsamplespval,
int nmingo,
int nmingolevel,
java.lang.String szextraval,
java.lang.String szcategoryIDval,
boolean bspotincluded,
java.lang.String szevidenceval,
java.lang.String sztaxonval,
boolean bpontoval,
boolean bcontoval,
boolean bfontoval,
boolean brandomgoval)
Consructor just calls parent constructor |
Method Summary |
void |
computeBestPvaluesClustersProfiles(STEM_DataSet theDataSet)
Loads theRecIDpval and theClusterRecIDpval to have the p-values for
the most enriched profiles and clusters for each category |
GoAnnotations.GoResults |
getCategory(java.util.ArrayList profileList,
java.util.ArrayList[] ids,
java.lang.String[] genenames,
java.util.ArrayList[] assignments,
boolean bqueryset,
java.util.HashSet htinames)
Used to get the GO results for a cluster of profiles
the id of each profile in the cluster is listed in profileList
an array list in ids has all the indicies in genenames
assigned to the profile
If bqueryset is true, then only genes also in the query set will be used
If htinames is non-null, then only genes also in htinames will be used |
void |
getProfileRankings(java.util.ArrayList clustersofprofilesnum,
java.util.ArrayList[] profilesAssigned,
java.lang.String[] genenames,
java.util.ArrayList[] assignments,
double[] expectedassignments)
Puts in tpgr a sorted ranking of profiles based on the current sort by seelctions |
Methods inherited from class edu.cmu.cs.sb.core.GoAnnotations |
addgenesgo, addgenesgocategory, addOfficialLine, addprobegenemap, buildxref, computePValues, computePValues, computePValuesBase, containsTaxon, geneIsOfType, getCategory, getCategory, getCategory, getCategory, getgocategories, getLevel, hashtoList1, hashtoList2, incrementSelectData, isOrder, labelsForID, levelGO, loadID, loadIDbase, loadIDCategory, printLevel, updateBest, updateBestHyperBinom, validEvidence |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
STEM_GoAnnotations
public STEM_GoAnnotations(java.lang.String szorganismsourceval,
java.lang.String szxrefsourceval,
java.lang.String szxrefval,
java.lang.String szGoFile,
java.lang.String szGoCategoryFile,
java.lang.String[] baseGenes1,
java.lang.String[] baseProbes1,
int nsamplespval,
int nmingo,
int nmingolevel,
java.lang.String szextraval,
java.lang.String szcategoryIDval,
boolean bspotincluded,
java.lang.String szevidenceval,
java.lang.String sztaxonval,
boolean bpontoval,
boolean bcontoval,
boolean bfontoval,
boolean brandomgoval)
throws java.io.FileNotFoundException,
java.io.IOException,
java.lang.IllegalArgumentException
- Consructor just calls parent constructor
- Throws:
java.io.FileNotFoundException
java.io.IOException
java.lang.IllegalArgumentException
getCategory
public GoAnnotations.GoResults getCategory(java.util.ArrayList profileList,
java.util.ArrayList[] ids,
java.lang.String[] genenames,
java.util.ArrayList[] assignments,
boolean bqueryset,
java.util.HashSet htinames)
- Used to get the GO results for a cluster of profiles
the id of each profile in the cluster is listed in profileList
an array list in ids has all the indicies in genenames
assigned to the profile
If bqueryset is true, then only genes also in the query set will be used
If htinames is non-null, then only genes also in htinames will be used
getProfileRankings
public void getProfileRankings(java.util.ArrayList clustersofprofilesnum,
java.util.ArrayList[] profilesAssigned,
java.lang.String[] genenames,
java.util.ArrayList[] assignments,
double[] expectedassignments)
- Puts in tpgr a sorted ranking of profiles based on the current sort by seelctions
computeBestPvaluesClustersProfiles
public void computeBestPvaluesClustersProfiles(STEM_DataSet theDataSet)
- Loads theRecIDpval and theClusterRecIDpval to have the p-values for
the most enriched profiles and clusters for each category