Pathway-class: Pathway Class

In CancerInSilico: An R interface for computational modeling of tumor progression

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

CancerInSilico documentation built on Nov. 8, 2020, 6:32 p.m.