analyzeQuantification: Perform quantitative analysis on the MPRA data. This analysis...

Description Usage Arguments Value Examples

View source: R/analysisFunctions.R

Description

Usage

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

Arguments

obj

the MpraObject

dnaDesign

the design of the DNA counts

rnaDesign

the design of the RNA counts

BPPARAM

a parallelization object created by BiocParallel. This overwrites the BPPARAM object set in the object creation.

Value

the MpraObject, with populated models

Examples

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data <- simulateMPRA(tr = rep(2,10), 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)

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