enhancerDataObject: enhancerDataObject Constructor

In ndukler/superEnhancerModelR: superEnhancerModelR

Description

Contructs a simple kinetic model object from synthesis and degredation rates

Usage

enhancerDataObject(expressionData, designInfo, activityFunction,
  errorModel = c("lognormal", "gaussian"), linkFunction = c("additive",
  "exponential", "logistic"), activityParameterBounds = c(-150, 150),
  errorParameterBounds = c(10^-3, 10^3),
  scaleParameterBounds = c(10^-3, 10^3))

Arguments

expressionData	A numeric vector with expression data, one entry for each row in the designInfo matrix
designInfo	A 0/1 (absence/presence) coded matrix with one column for each enhancer and one row for each experiment
activityFunction	the formula for the activity function (e.g. ~ E1 + E2 + E1*E2)
errorModel	Desired error model for the regression function. Currently only lognormal or gaussian.
linkFunction	Function that converts activity to gene expression
activityParameterBounds	sets upper and lower bounds for coefficients of activity function - c(lower,upper)
errorParameterBounds	sets upper and lower bounds for the error parameter - c(lower,upper)
scaleParameterBounds	sets upper and lower bounds for the saturation parameter (only in logistic model) - c(lower,upper)

Examples

## Create a test design data.frame
design=expand.grid(E1=c(0,1),E2=c(0,1),E3=c(0,1))
## Create fake expression data
expression=c(0.001,0.2,0.3,0.7,0.4,0.8,0.6,1)*100
## Create activity function
actFun=formula(~E1+E2+E3+E1:E2)
edo = enhancerDataObject(expression,design,actFun)

ndukler/superEnhancerModelR documentation built on May 17, 2019, 8:18 p.m.