ToPASeq (version 1.6.0)

makeDefautEdgeData: Creates auxiliary data needed for SPIA method

Description

This function creates a list containing auxiliary data needed in SPIA method for conversion between edge types and dividing interaction into three categories: positive, negative and neutral

Usage

makeDefaultEdgeData

Value

A list of two data frames explained in the Details The format is: List of 2 $ graphite2SPIA: chr [1:26, 1:2] "binding" "control(In(ACTIVATION))" "control(In(INHIBITION))" "control(Out(ACTIVATION))" ... ..- attr(*, "dimnames")=List of 2 .. ..$ : NULL .. ..$ : chr [1:2] "type" "spiaType" $ beta :'data.frame': 25 obs. of 2 variables: ..$ rel : chr [1:25] "activation" "compound" "binding/association" "expression" ... ..$ beta: num [1:25] 1 0 0 1 -1 1 0 -1 -1 0 ...

Source

The data are manualy cerated from the unexported objects from graphite package version 1.10.1.

Details

The first slot called graphite2SPIA contains a mapping table between edge types in topologies from graphite and edge types which are used in the implementation of SPIA in SPIA package. All of the edge types present in the topologies must be also covered by this table otherwise the method could not be applied.

The second slot called beta divides the 25 interaction types into three categories: positive (beta=1), negative (beta=-1 and neutral (beta=0) in the sense of gene regulation. Only user familiar with all the details of SPIA should change this.

Examples

str(makeDefaultEdgeData())