getancestors - Class: geneont

Find terms that are ancestors of specified Gene Ontology (GO) term

Syntax

AncestorIDs = getancestors(GeneontObj, ID) [AncestorIDs, Counts] = getancestors(GeneontObj, ID) ... = getancestors(..., 'Height', HeightValue, ...) ... = getancestors(..., 'Relationtype', RelationtypeValue, ...) ... = getancestors(..., 'Exclude', ExcludeValue, ...)

Description

AncestorIDs = getancestors(GeneontObj, ID) searches GeneontObj, a geneont object, for GO terms that are ancestors of the GO term(s) specified by ID, which is a GO term identifier or vector of identifiers. It returns AncestorIDs, a vector of GO term identifiers including ID. ID is a nonnegative integer or a vector containing nonnegative integers.

[AncestorIDs, Counts] = getancestors(GeneontObj, ID) also returns the number of times each ancestor is found. Counts is a column vector with the same number of elements as terms in GeneontObj.

Tip The Counts return value is useful when you tally counts in gene enrichment studies. For more information, see the Gene Ontology Enrichment in Microarray Data demo.

... = getancestors(..., 'PropertyName', PropertyValue, ...) calls getancestors with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

... = getancestors(..., 'Height', HeightValue, ...) searches up through a specified number of levels, HeightValue, in the gene ontology. HeightValue is a positive integer. Default is Inf.

... = getancestors(..., 'Relationtype', RelationtypeValue, ...) searches for specified relationship types, RelationtypeValue, in the gene ontology. RelationtypeValue is a string. Choices are 'is_a', 'part_of', or 'both' (default).

... = getancestors(..., 'Exclude', ExcludeValue, ...) controls excluding ID, the original queried term(s), from the output AncestorIDs, unless the term was reached while searching the gene ontology. Choices are true or false (default).

Inputs

`GeneontObj`	A geneont object, such as created by the `geneont` constructor function.
`ID`	GO term identifier or vector of identifiers.
`HeightValue`	Positive integer specifying the number of levels to search upward in the gene ontology.
`RelationtypeValue`	String specifying the relationship types to search for in the gene ontology. Choices are: `'is_a'` `'part_of'` `'both'` (default)
`ExcludeValue`	Controls excluding `ID`, the original queried term(s), from the output `AncestorIDs`, unless the term was reached while searching the gene ontology. Choices are `true` or `false` (default).

Outputs

`AncestorIDs`	Vector of GO term identifiers including `ID`.
`Counts`	Column vector with the same number of elements as terms in `GeneontObj`, indicating the number of times each ancestor is found.

Examples

Download the current version of the Gene Ontology database from the Web into a geneont object in the MATLAB software.
```
GO = geneont('LIVE', true)
```
The MATLAB software creates a geneont object and displays the number of terms in the database.
```
Gene Ontology object with 24316 Terms.
```

Retrieve the ancestors of the Gene Ontology term with an identifier of 46680.

ancestors = getancestors(GO,46680)

ancestors =
        8150
        9636
       17085
       42221
       46680
       50896

Create a subordinate Gene Ontology.

subontology = GO(ancestors)

Gene Ontology object with 6 Terms.

Create and display a report of the subordinate Gene Ontology terms, that includes the GO identifier and name.

rpt = get(subontology.terms,{'id','name'})

    [ 8150]    'biological_process'
    [ 9636]    'response to toxin' 
    [17085]             [1x23 char]
    [42221]             [1x29 char]
    [46680]    'response to DDT'   
    [50896]             [1x20 char]

View relationships of the subordinate Gene Ontology by using the getmatrix method to create a connection matrix to pass to the biograph function.
```
cm = getmatrix(subontology);
BG = biograph(cm, get(subontology.terms, 'name'));
view(BG)
```