GOroot2TermPaths: Function to get all paths from the gene ontology root of the...
In CLippmann/dbtORA: Overrepresentation Analysis
Description
Usage
Arguments
Value
Author(s)
View source: R/GOroot2TermPaths.R
Description
Function to get all paths from the gene ontology root of the DAG to one target term.
Usage
1
GOroot2TermPaths(TargetTerm, AdjMatrix, GOtermNr, GOroot = 8150)
Arguments
TargetTerm
Numeric;
GO term number of the term that the paths should be found for.
AdjMatrix
Numeric;
Adjacency matrix of (only) all ancestors of TargetTerm and TargetTerm itself.
AdjMatrix[i,j] == 1 iff there exists an edge in
GO-DAG from node i to node j (i is parent of j).
GOtermNr
Numeric;
Vector of GO term numbers corresponding to rows and columns of AdjMatrix.
Has to contain TargetTerm.
GOroot
Numeric; Default = 8150
The GO term number of the root of the ontology in which the target term
and all GOtermNrs are. One of:
8150 for biological process,
3674 for molecular function or
5575 for cellular component.
Value
Taxonomy
Numeric;
A list of indices such that GOtermNr[Taxonomy[[i]]] is the i-th path from
GOroot to TargetTerm.
Author(s)
CL
CLippmann/dbtORA documentation built on Feb. 4, 2020, 12:37 a.m.
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Description Usage Arguments Value Author(s)
View source: R/GOroot2TermPaths.R
Description
Function to get all paths from the gene ontology root of the DAG to one target term.
Usage
1 | GOroot2TermPaths(TargetTerm, AdjMatrix, GOtermNr, GOroot = 8150)
|
Arguments
TargetTerm |
Numeric; GO term number of the term that the paths should be found for. |
AdjMatrix |
Numeric; Adjacency matrix of (only) all ancestors of TargetTerm and TargetTerm itself. AdjMatrix[i,j] == 1 iff there exists an edge in GO-DAG from node i to node j (i is parent of j). |
GOtermNr |
Numeric; Vector of GO term numbers corresponding to rows and columns of AdjMatrix. Has to contain TargetTerm. |
GOroot |
Numeric; Default = 8150 The GO term number of the root of the ontology in which the target term and all GOtermNrs are. One of: 8150 for biological process, 3674 for molecular function or 5575 for cellular component. |
Value
Taxonomy |
Numeric;
A list of indices such that GOtermNr[Taxonomy[[i]]] is the i-th path from
|
Author(s)
CL
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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