estimateDispersions: Estimate Dispersions Using DESeq2

In ndukler/tkSim: Simulates transcript abundance based on synthesis and degredation rates

Description

Estimates the dispersions for each gene using DESeq2. Overwrites the existing dipersion model in the supplied basicKinetic Model and then returns the object. If byGene = TRUE then a function returning a single dispersion estimate for each gene will be set to @dispersionModel. If FALSE then a general function that gives a dispersion estimate for a given mean using the composite information from all genes, time points, and replicates will be set to @dispersionModel.

Usage

## S4 method for signature 'basicKineticModel'
estimateDispersions(object, byGene = T)

Arguments

object	A basicKineticModel object
byGene	Boolean controlling fuction return value. See description or value for more information

Value

If byGene = TRUE then a function that takes a gene index and returns a single dispersion estimate for that gene. If FALSE then a general function will be returned that gives a dispersion estimate for a given read value (assumed to be the mean of the distribution) using the composite information from all genes, time points, and replicates.

ndukler/tkSim documentation built on May 16, 2019, 8:12 p.m.