analyzeQuantification {MPRAnalyze}R Documentation

Perform quantitative analysis on the MPRA data. This analysis aims to determine which sequences have a regulatory function, when no condition is being tested.

Description

Usage

analyzeQuantification(obj, dnaDesign = ~1, rnaDesign = ~1)

Arguments

obj

the MpraObject

dnaDesign

the design of the DNA counts

rnaDesign

the design of the RNA counts

Value

the MpraObject, with populated models

Examples

data <- simulateMPRA(tr = rep(2,10), da=NULL, nbatch=2, nbc=15)
obj <- MpraObject(dnaCounts = data$obs.dna, 
                  rnaCounts = data$obs.rna, 
                  colAnnot = data$annot)
obj <- estimateDepthFactors(obj, lib.factor = "batch", which.lib = "both")
obj <- analyzeQuantification(obj, dnaDesign = ~ batch + barcode, 
                              rnaDesign = ~1)

[Package MPRAnalyze version 1.2.0 Index]