extractModelParameters: extract the DNA model parameters
In YosefLab/MPRAnalyze: Statistical Analysis of MPRA data

Description Usage Arguments Value Examples

extract the DNA model parameters

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getModelParameters_DNA(obj, features = NULL, full = TRUE)

getModelParameters_RNA(obj, features = NULL, full = TRUE)

`obj`	the MpraObject to extract the parameters from
`features`	the features to extract the parameters from (by default, parameters will be returned for all features)
`full`	if TRUE (default), return the parameters of the full model. Otherwise, return the parameters of the reduced model (only relevant for LRT-based analyses)

a data.frame of features (rows) by parameters (cols). By convension, the first parameter is related to the second moment, and the interpretation of it depends on the distributional model used ('alpha' for 'gamma.pois', variance for 'ln.nb' and 'ln.ln')

data <- simulateMPRA(tr = rep(2,5), 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)
model.params.dna <- getModelParameters_DNA(obj)
model.params.rna <- getModelParameters_RNA(obj)