setModel: Set the distributional model used. Default is gamma.pois, and...

In YosefLab/MPRAnalyze: Statistical Analysis of MPRA data

Description

Set the distributional model used. Default is gamma.pois, and is recommended. Other supoprted models are ln.nb in which the DNA follows a log-normal distribution and the RNA follows a negative binomial, and ln.ln in which both follow log-normal distributions. To use alternative distributional models, use this function before fitting the model.

Usage

setModel(obj, model)

Arguments

obj	the MPRAnalyze object
model	the charater identifier of the model to be used. Currently supported models: "ln.nb", "gamma.pois", "ln.ln"

Value

the MPRAnalyze with the model set for the given value

Examples

data <- simulateMPRA(tr = rep(2,10), da=NULL, nbatch=2, nbc=20)
obj <- MpraObject(dnaCounts = data$obs.dna, 
                  rnaCounts = data$obs.rna, 
                  colAnnot = data$annot)
obj <- estimateDepthFactors(obj, lib.factor = "batch", which.lib = "both")
obj <- setModel(obj, "ln.ln")
obj <- analyzeQuantification(obj, dnaDesign = ~ batch + barcode, 
                              rnaDesign = ~1)

YosefLab/MPRAnalyze documentation built on Nov. 14, 2020, 2:35 a.m.