BIOS: geneOntology.h Source File

00001 #ifndef DEF_GENE_ONTOLOGY_H
00002 #define DEF_GENE_ONTOLOGY_H
00003 
00004 
00011 #define MULTIPLE_TESTING_CORRECTION_BENJAMINI_HOCHBERG 1
00012 #define MULTIPLE_TESTING_CORRECTION_BONFERRONI 2
00013 
00014 
00015 
00019 typedef struct {
00020   char* tag;
00021   char* value;
00022 } GoTagValue;
00023 
00024 
00025 
00029 typedef struct {
00030   char* id;
00031   char* name;
00032   char* namespace;
00033   Texta altIds;
00034   char* definition;
00035   Texta synonyms;
00036   Texta subsets;
00037   int isGenericGoSlim;
00038   char* comment;
00039   int isObsolete;
00040   Texta considers;
00041   Array xrefs; // of type TagValue
00042   Array relationships; // of type TagValue
00043   Texta parents;
00044 } GoTerm;
00045 
00046 
00047 
00051 typedef struct {
00052   char* id;
00053   GoTerm *goTerm;
00054   Array parents; // of type GoNode*
00055   Array children; // of type GoNode*
00056   Texta associatedGenes;
00057   Texta genesOfInterest;
00058 } GoNode;
00059 
00060 
00061 
00065 typedef struct {
00066   char* db;
00067   char* dbGeneName;
00068   char* geneName;
00069   Texta goIds;
00070 } GoGeneAssociation;
00071 
00072 
00073 
00077 typedef struct {
00078   GoNode* goNode;
00079   Texta genesOfInterest; // Names of the genes of interest of goNode and its children
00080   int numberOfAnnotatedGenes;
00081   int numberOfGenesOfInterest;
00082   double pvalue;
00083   double pvalueCorrected;
00084 } GoStatistic;
00085 
00086 
00087 
00088 extern void geneOntology_init (char* geneOntologyFileName);
00089 extern void geneOntology_mapGeneAnnotationsToGeneOntology (char* goGeneAssociationFileName);
00090 extern Texta geneOntology_mapGenesOfInterestToGeneOntology (Texta genesOfInterest);
00091 extern GoNode* geneOntology_getBiologicalProcessRoot (void);
00092 extern GoNode* geneOntology_getMolecularFunctionRoot (void);
00093 extern GoNode* geneOntology_getCellularComponentRoot (void);
00094 extern Array geneOntology_getBiologicalProcessGoNodes (void);
00095 extern Array geneOntology_getMolecularFunctionGoNodes (void);
00096 extern Array geneOntology_getCellularComponentGoNodes (void);
00097 extern Array geneOntology_getGenericGoSlimNodes (void);
00098 extern Array geneOntology_getAllGoNodes (void);
00099 extern int geneOntology_getNumberOfAssociatedGenes (void);
00100 extern int geneOntology_getNumberOfGenesOfInterest (void);
00101 extern void geneOntology_resetGenesOfInterest (void);
00102 extern GoNode* geneOntology_findGoNode (char* id);
00103 extern GoGeneAssociation* geneOntology_findGoGeneAssociation (char* geneName);
00104 extern Array geneOntology_calculateGeneEnrichment (Array goNodePointers, int multipleTestingCorrectionMethod);
00105 extern Array geneOntology_calculateGeneDepletion (Array goNodePointers, int multipleTestingCorrectionMethod);
00106 extern Array geneOntology_getChildrenAtSpecifiedHierarchyLevel (GoNode* currGoNode, int level);
00107 
00108 
00109 
00110 #endif