Pathway-class {CancerInSilico} | R Documentation

## Pathway Class

### Description

Describes the basic properties of a gene pathway

### Usage

    ## S4 method for signature 'Pathway'
    initialize(.Object, ...)

### Arguments

`.Object` | Pathway object
`...` | extra arguments for constructor

### Details

expressionScale is a function that accepts three arguments: model, cell, and time. It should return a number in [0,1] that describes how active the genes are in this pathway for a given cell in the model at a given time. In bulk data, the pathway activity is averaged and transformed by 1 / (1 + exp(-k * (x - M))) where k = transformSlope and M = transformMidpoint. The scale determines how expressed genes in this pathway are. i.e. and scale of 0 means all genes will have minExpression value and a scale of 1 means all genes will have maxExpression value. In between these values the gene expression scales linearly.

### Value

constructed object

### Slots

`genes`

  names of genes in the pathway

`expressionScale`

  function descibing how this pathway is affected by the state of the model

`minExpression`

  minimum expression value for each gene (vector)

`maxExpression`

  maximum expression value for each gene (vector)

`transformSlope`

  parameter for transforming bulk data

`transformMidpoint`

  parameter for transforming bulk data

[Package CancerInSilico version 2.14.0 Index]