geneOntology.h File Reference

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Data Structures

struct GoGeneAssociation

GoGeneAssociation. More...

struct GoNode

GoNode. More...

struct GoStatistic

GoStatistic. More...

struct GoTagValue

GoTagValue. More...

struct GoTerm

GoTerm. More...

Functions

Array geneOntology_calculateGeneDepletion (Array goNodePointers, int multipleTestingCorrectionMethod)

Calculate the gene depletion for every GoNode in goNodePointers.

Array geneOntology_calculateGeneEnrichment (Array goNodePointers, int multipleTestingCorrectionMethod)

Calculate the gene enrichment for every GoNode in goNodePointers.

GoGeneAssociation * geneOntology_findGoGeneAssociation (char *geneName)

Find a GoGeneAssociation.

GoNode * geneOntology_findGoNode (char *id)

Find a GoNode.

Array geneOntology_getAllGoNodes (void)

Get the GoNodes of the entire ontology.

Array geneOntology_getBiologicalProcessGoNodes (void)

Get the GoNodes that are part of the biological_process hierarchy.

GoNode * geneOntology_getBiologicalProcessRoot (void)

Get the GoNode that points to the biological_process root.

Array geneOntology_getCellularComponentGoNodes (void)

Get the GoNodes that are part of the cellular_component hierarchy.

GoNode * geneOntology_getCellularComponentRoot (void)

Get the GoNode that points to the cellular_component root.

Array geneOntology_getChildrenAtSpecifiedHierarchyLevel (GoNode *currGoNode, int level)

Get the children of a GoNode at a specified hiearchy level.

Array geneOntology_getGenericGoSlimNodes (void)

Get the generic GO slim nodes.

Array geneOntology_getMolecularFunctionGoNodes (void)

Get the GoNodes that are part of the molecular_function hierarchy.

GoNode * geneOntology_getMolecularFunctionRoot (void)

Get the GoNode that points to the molecular_function root.

int geneOntology_getNumberOfAssociatedGenes (void)

Get the number of associated genes.

int geneOntology_getNumberOfGenesOfInterest (void)

Get the number of genes of interest that have been mapped to the gene ontology.

void geneOntology_init (char *geneOntologyFileName)

Initialize the geneOntology module.

void geneOntology_mapGeneAnnotationsToGeneOntology (char *goGeneAssociationFileName)

Map gene annotations to the gene ontology.

Texta geneOntology_mapGenesOfInterestToGeneOntology (Texta genesOfInterest)

Map genes of interest to the gene ontology.

void geneOntology_resetGenesOfInterest (void)

Resets (performs arrayClear()) the genes of interest for every GoNode.

Detailed Description

Author:: Lukas Habegger (lukas.habegger@yale.edu)

Definition in file geneOntology.h.

Function Documentation

Array geneOntology_calculateGeneDepletion	(	Array	goNodePointers,
		int	multipleTestingCorrectionMethod
	)

Calculate the gene depletion for every GoNode in goNodePointers.

Parameters:

`[in]`	goNodePointers	Array of goNode pointers. Gene depletion is calculated for every goNode in this Array.
`[in]`	multipleTestingCorrectionMethod	Specifies the multiple testing correction method. Use either MULTIPLE_TESTING_CORRECTION_BENJAMINI_HOCHBERG or MULTIPLE_TESTING_CORRECTION_BONFERRONI.

Returns:: Array of type GoStatistic. This array is sorted by pvalue in ascending order.

Precondition:

The geneOntolgy module has been initialized. See geneOntology_init()

The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

The genes of interest have been mapped to the gene ontology. See geneOntology_mapGenesOfInterestToGeneOntology()

Definition at line 822 of file geneOntology.c.

Array geneOntology_calculateGeneEnrichment	(	Array	goNodePointers,
		int	multipleTestingCorrectionMethod
	)

Calculate the gene enrichment for every GoNode in goNodePointers.

Parameters:

`[in]`	goNodePointers	Array of goNode pointers. Gene enrichment is calculated for every goNode in this Array.
`[in]`	multipleTestingCorrectionMethod	Specifies the multiple testing correction method. Use either MULTIPLE_TESTING_CORRECTION_BENJAMINI_HOCHBERG or MULTIPLE_TESTING_CORRECTION_BONFERRONI.

Returns:: Array of type GoStatistic. This array is sorted by pvalue in ascending order.

Precondition:

The geneOntolgy module has been initialized. See geneOntology_init()

The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

The genes of interest have been mapped to the gene ontology. See geneOntology_mapGenesOfInterestToGeneOntology()

Definition at line 802 of file geneOntology.c.

GoGeneAssociation* geneOntology_findGoGeneAssociation ( char * geneName )

Find a GoGeneAssociation.

Parameters:

[in] geneName A geneName or geneSymbol as specified in the geneAssociation file. See http://www.geneontology.org/GO.format.annotation.shtml for details. This geneName refers to the third column labeled as DB_Object_Symbol.

Returns:: A pointer to the GoGeneAssociation, NULL if GoGeneAssociation was not found

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()
The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

Definition at line 554 of file geneOntology.c.

GoNode* geneOntology_findGoNode ( char * id )

Find a GoNode.

Parameters:

[in] id A GO term identifier. Example: GO:0065003

Returns:: A pointer to the GoNode, NULL if the GO term was not found

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 365 of file geneOntology.c.

Array geneOntology_getAllGoNodes ( void )

Get the GoNodes of the entire ontology.

Returns:: An Array of GoNode pointers

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 143 of file geneOntology.c.

Array geneOntology_getBiologicalProcessGoNodes ( void )

Get the GoNodes that are part of the biological_process hierarchy.

Returns:: An Array of GoNode pointers

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 107 of file geneOntology.c.

GoNode* geneOntology_getBiologicalProcessRoot ( void )

Get the GoNode that points to the biological_process root.

Returns:: A GoNode pointer

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 47 of file geneOntology.c.

Array geneOntology_getCellularComponentGoNodes ( void )

Get the GoNodes that are part of the cellular_component hierarchy.

Returns:: An Array of GoNode pointers

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 131 of file geneOntology.c.

GoNode* geneOntology_getCellularComponentRoot ( void )

Get the GoNode that points to the cellular_component root.

Returns:: A GoNode pointer

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 71 of file geneOntology.c.

Array geneOntology_getChildrenAtSpecifiedHierarchyLevel	(	GoNode *	currGoNode,
		int	level
	)

Get the children of a GoNode at a specified hiearchy level.

Parameters:

`[in]`	currGoNode	Get the children of this GoNode at the specified hiearchy level.
`[in]`	level	Specifies the level within the gene ontology relative to the currGoNode. The level of currGoNode is 0. Example: To get the grand-children of currGoNode the level would be 2.

Returns:: An Array of GoNode pointers.

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 868 of file geneOntology.c.

Array geneOntology_getGenericGoSlimNodes ( void )

Get the generic GO slim nodes.

Returns:: An Array of GoNode pointers

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Note:: The memory belongs to this module

Definition at line 156 of file geneOntology.c.

Array geneOntology_getMolecularFunctionGoNodes ( void )

Get the GoNodes that are part of the molecular_function hierarchy.

Returns:: An Array of GoNode pointers

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 119 of file geneOntology.c.

GoNode* geneOntology_getMolecularFunctionRoot ( void )

Get the GoNode that points to the molecular_function root.

Returns:: A GoNode pointer

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 59 of file geneOntology.c.

int geneOntology_getNumberOfAssociatedGenes ( void )

Get the number of associated genes.

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()
The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

Definition at line 169 of file geneOntology.c.

int geneOntology_getNumberOfGenesOfInterest ( void )

Get the number of genes of interest that have been mapped to the gene ontology.

Note: duplicates gene names were removed.

Precondition:

The geneOntolgy module has been initialized. See geneOntology_init()

The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

The genes of interest have been mapped to the gene ontology. See geneOntology_mapGenesOfInterestToGeneOntology()

Definition at line 185 of file geneOntology.c.

void geneOntology_init ( char * geneOntologyFileName )

Initialize the geneOntology module.

Parameters:

[in] geneOntologyFileName File that describes the entire gene ontology. This file has to be in OBO format. See http://www.geneontology.org/GO.format.obo-1_2.shtml for details.

Definition at line 619 of file geneOntology.c.

void geneOntology_mapGeneAnnotationsToGeneOntology ( char * goGeneAssociationFileName )

Map gene annotations to the gene ontology.

Parameters:

[in] goGeneAssociationFileName File that maps the genes of a specific organism to the gene ontology. This file has to be in GO Annotation format. See http://www.geneontology.org/GO.format.annotation.shtml for details.

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()

Definition at line 633 of file geneOntology.c.

Texta geneOntology_mapGenesOfInterestToGeneOntology ( Texta geneNamesOfInterest )

Map genes of interest to the gene ontology.

Parameters:

[in] genesNamesOfInterest Texta that contains the gene names of the genes of interest. The gene names must be consistent with the genes names found in the gene annotation file.

Returns:: Texta of invalid gene names. If the number of invalid gene names is zero, then an empty Texta is returned.

Precondition:: The geneOntolgy module has been initialized. See geneOntology_init()
The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

Definition at line 580 of file geneOntology.c.

void geneOntology_resetGenesOfInterest ( void )

Resets (performs arrayClear()) the genes of interest for every GoNode.

Precondition:

The geneOntolgy module has been initialized. See geneOntology_init()

The gene annotations have been mapped to the gene ontology. See geneOntology_mapGeneAnnotationsToGeneOntology()

The genes of interest have been mapped to the gene ontology. See geneOntology_mapGenesOfInterestToGeneOntology()

Postcondition:: A new set of genes of interest can be mapped to the gene ontology by using geneOntology_mapGenesOfInterestToGeneOntology()

Definition at line 202 of file geneOntology.c.


Data Structures
struct	GoGeneAssociation
	GoGeneAssociation. More...
struct	GoNode
	GoNode. More...
struct	GoStatistic
	GoStatistic. More...
struct	GoTagValue
	GoTagValue. More...
struct	GoTerm
	GoTerm. More...
Functions
Array	geneOntology_calculateGeneDepletion (Array goNodePointers, int multipleTestingCorrectionMethod)
	Calculate the gene depletion for every GoNode in goNodePointers.
Array	geneOntology_calculateGeneEnrichment (Array goNodePointers, int multipleTestingCorrectionMethod)
	Calculate the gene enrichment for every GoNode in goNodePointers.
GoGeneAssociation *	geneOntology_findGoGeneAssociation (char *geneName)
	Find a GoGeneAssociation.
GoNode *	geneOntology_findGoNode (char *id)
	Find a GoNode.
Array	geneOntology_getAllGoNodes (void)
	Get the GoNodes of the entire ontology.
Array	geneOntology_getBiologicalProcessGoNodes (void)
	Get the GoNodes that are part of the biological_process hierarchy.
GoNode *	geneOntology_getBiologicalProcessRoot (void)
	Get the GoNode that points to the biological_process root.
Array	geneOntology_getCellularComponentGoNodes (void)
	Get the GoNodes that are part of the cellular_component hierarchy.
GoNode *	geneOntology_getCellularComponentRoot (void)
	Get the GoNode that points to the cellular_component root.
Array	geneOntology_getChildrenAtSpecifiedHierarchyLevel (GoNode *currGoNode, int level)
	Get the children of a GoNode at a specified hiearchy level.
Array	geneOntology_getGenericGoSlimNodes (void)
	Get the generic GO slim nodes.
Array	geneOntology_getMolecularFunctionGoNodes (void)
	Get the GoNodes that are part of the molecular_function hierarchy.
GoNode *	geneOntology_getMolecularFunctionRoot (void)
	Get the GoNode that points to the molecular_function root.
int	geneOntology_getNumberOfAssociatedGenes (void)
	Get the number of associated genes.
int	geneOntology_getNumberOfGenesOfInterest (void)
	Get the number of genes of interest that have been mapped to the gene ontology.
void	geneOntology_init (char *geneOntologyFileName)
	Initialize the geneOntology module.
void	geneOntology_mapGeneAnnotationsToGeneOntology (char *goGeneAssociationFileName)
	Map gene annotations to the gene ontology.
Texta	geneOntology_mapGenesOfInterestToGeneOntology (Texta genesOfInterest)
	Map genes of interest to the gene ontology.
void	geneOntology_resetGenesOfInterest (void)
	Resets (performs arrayClear()) the genes of interest for every GoNode.