CHRONOS (version 1.0.3)

getEdgeTypes: 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.

Value

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

Details

Edge types llllllll{ activation 1 inhibition 2 apathetic 3 no interaction 4 } Default interaction - edge type mapping rrrrrr{ 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 } rrrrrr{ 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 }

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