getEdgeTypes {CHRONOS} | R Documentation

## Map various types of gene-gene interactions in KGML files to edge types in corresponding pathway graphs.

### Description

Map various types of gene-gene interactions in KGML files to edge types in corresponding pathway graphs.

### Usage

    getEdgeTypes(type)

### Arguments

`type` | A vector of interaction types.

### Details

Edge types

activation | 1 | inhibition | 2 | apathetic | 3 | no interaction | 4

Default interaction - edge type mapping

01 | unknown | 3 | 02 | activation | 1
03 | inhibition | 2 | 04 | binding/association | 3
05 | expression | 1 | 06 | repression | 2
07 | phosphorylation | 3 | 08 | dephosphorylation | 3
09 | ubiquitination | 3 | 10 | dissociation | 3
11 | indirect effect | 3 | 12 | state change | 3
13 | compound | 3 | 14 | hidden compound | 3
16 | missing interaction | 3 | 16 | activation_phosphorylation | 1
17 | activation_dephosphorylation | 1 | 18 | activation_ubiquitination | 1
19 | activation_indirect effect | 1 | 20 | activation_binding/association | 1
21 | activation_inhibition | 3 | 22 | activation_methylation | 1
23 | inhibition_phosphorylation | 2 | 24 | inhibition_dephosphorylation | 2
25 | inhibition_ubiquitination | 2 | 26 | inhibition_indirect effect | 2
27 | inhibition_binding/association | 2 | 28 | inhibition_expression | 2
29 | inhibition_methylation | 2 | 30 | compound_expression | 1
31 | compound_activation | 1 | 32 | compound_inhibition | 2

33 | compound_activation_indirect effect | 1
34 | compound_activation_phosphorylation | 1
35 | phosphorylation_indirect effect | 3
36 | phosphorylation_binding/association | 3
37 | phosphorylation_dissociation | 3
38 | dephosphorylation_indirect effect | 3
39 | binding/association_missing interaction | 3
40 | binding/association_indirect effect | 3
41 | expression_indirect effect | 1
42 | repression_indirect effect | 2
43 | ubiquitination_inhibition | 2
44 | dissociation_missing interaction | 3
45 | indirect effect_phosphorylation | 3 |  |
46 | activation_phosphorylation_binding/association | 1
47 | activation_phosphorylation_indirect effect | 1

### Value

If an interaction type has been supplied, the corresponging edge types are returned. If not, the complete mapping is returned.

### Examples

    # Example 1

    # Retreive edge types for phosphorylation and dephosphorylation.
    getEdgeTypes(c(7,8))

    # Example 2

    # Returns a data frame containing the innteraction - edge type mapper.
    types <- getEdgeTypes()

    # Set phosphorylation to inhibition.
    types[8,2] <- 2

[Package CHRONOS version 1.15.1 Index]