getEdgeTypes: Map various types of gene-gene interactions in KGML files to...

In CHRONOS: CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

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

CHRONOS documentation built on Nov. 8, 2020, 8:30 p.m.