compareSteady: Generate an object of class INSPEcT_diffsteady from two...

Description Usage Arguments Value Examples

Description

Generate an object of class INSPEcT_diffsteady from two objects of class INSPEcT

This method compares two object of class INSPEcT in order to identify differential usage of synthesis, processing or degradation rates in two different steady-state conditions. The two INSPEcT objects must have been profiled with replicates in order to provide a statistical significance to the differences between their rates.

Usage

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compareSteady(inspectIds1, inspectIds2, nRep1, nRep2)

## S4 method for signature 'INSPEcT,INSPEcT,numeric,numeric'
compareSteady(inspectIds1,
  inspectIds2, nRep1, nRep2)

Arguments

inspectIds1

An object of calss INSPEcT

inspectIds2

A second object of calss INSPEcT

nRep1

number of replicates of the first object

nRep2

number of replicates of the second object

Value

An object of class INSPEcT_diffsteady which contains both the absolute quantification of the rates as well as the comparison with the statistical significance associated for each gene and rate. (See INSPEcT_diffsteady-class)

Examples

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data('nascentInspObj', package='INSPEcT')	
simRates<-makeSimModel(nascentInspObj, 1000, seed=1)
newTpts<-c(0, 16)
nascentInspObj_sim3<-makeSimDataset(object=simRates
                                   ,tpts=newTpts
                                   ,nRep=3
                                   ,NoNascent=FALSE
                                   ,seed=1)
newTpts<-c(0, 16)
nascentInspObj_sim4<-makeSimDataset(object=simRates
                                   ,tpts=newTpts
                                   ,nRep=4
                                   ,NoNascent=FALSE
                                   ,seed=2)

diffrates<-compareSteady(inspectIds1=nascentInspObj_sim3
                        ,inspectIds2=nascentInspObj_sim4
                        ,nRep1=3
                        ,nRep2=4)
diffrates

ste-depo/INSPEcT documentation built on July 30, 2018, 12:04 p.m.