setEdgeWeights {ROntoTools} | R Documentation

## Set gene weights based on edge type

### Description

`setEdgeWeights`

### Usage

    setEdgeWeights(graphList, edgeTypeAttr = "subtype",
      edgeWeightByType = list(activation = 1, inhibition = -1, expression = 1,
      repression = -1), defaultWeight = 0, combineWeights = sum,
      nodeOnlyGraphs = FALSE)

### Arguments

`graphList` | a list of `graphNEL` objects
`edgeTypeAttr` | edge attribute to be considered as the edge type. If the edge has multiple types, the edge type attribute is considered as a comma separeted list of types
`edgeWeightByType` | named list of weigths, where the names of the list are the edge type (values of the attribute defined by `edgeTypeAttr`)
`defaultWeight` | default value for an edge with a type not defined in `edgeWeightByType`
`combineWeights` | for the edges with multiple types, the function to be applied on the vector of weights
`nodeOnlyGraphs` | boolean value marking if graphs with no edges should be returned or not; note that graphs with all edge weights equal to 0 are considered node only graphs

### Value

The `graphList` with the edge weights set.

### Author(s)

Calin Voichita and Sorin Draghici

### Examples

    # load the set of pathways
    kpg <- keggPathwayGraphs("hsa")

    kpg <- setEdgeWeights(kpg)

    edgeWeights(kpg[["path:hsa04110"]])

[Package ROntoTools version 2.18.0 Index]