getmatrix

Convert geneont object into relationship matrix

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Syntax

[Matrix] = getmatrix(GeneontObj)
[Matrix,ID] = getmatrix(GeneontObj)
[Matrix,ID,Relationship] = getmatrix(GeneontObj)

Description

[Matrix] = getmatrix(GeneontObj) converts a geneont object into a matrix of relationship values between nodes (row and column indices).

example

[Matrix,ID] = getmatrix(GeneontObj) also returns a column vector listing Gene Ontology IDs that correspond to the rows and columns of Matrix.

example

[Matrix,ID,Relationship] = getmatrix(GeneontObj) also returns a cell array of character vectors defining the types of relationships.

example

Examples

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Open Live Script

Download the current version of the Gene Ontology database from the Web into a geneont object.

GO = geneont('Live',true)
Gene Ontology object with 47266 Terms.

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

ancestors = getancestors(GO,46680)
ancestors = 8×1

        8150
        9636
       10033
       14070
       17085
       42221
       46680
       50896

Create a subordinate Gene Ontology.

GeneontObj = GO(ancestors)
Gene Ontology object with 8 Terms.

View the relationships in GeneontObj.

[Matrix,ID,Relationship] = getmatrix(GeneontObj)
Matrix = 
   (6,2)        1
   (6,3)        1
   (3,4)        1
   (2,5)        1
   (8,6)        1
   (4,7)        1
   (5,7)        1
   (1,8)        1


ID = 8×1

        8150
        9636
       10033
       14070
       17085
       42221
       46680
       50896


Relationship = 1×6 cell
    {'is_a'}    {'negatively_regulates'}    {'part_of'}    {'positively_regulates'}    {'regulates'}    {'term_tracker_item'}

Plot the relationships.

BG = digraph(Matrix,get(GeneontObj.terms,"name"));
plot(BG,Layout="force")

Figure contains an axes object. The axes object contains an object of type graphplot.

Input Arguments

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Gene ontology object, specified as the output of the geneont command.

Example: geneont('Live',true)

Output Arguments

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Relationship values between nodes (rows and columns) of GeneontObj, returned as a sparse matrix with the following entries:

  • 0 — No relationship

  • 1 — “is_a” relationship

  • 2 — “part_of” relationship

Gene ontology IDs, returned as a nonnegative integer column vector. The entries in ID correspond to the entries in Matrix.

Types of relationships, returned as a cell array of character vectors.

Version History

Introduced before R2006a

See Also

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