extractModelParameters: extract the DNA model parameters

Description Usage Arguments Value Examples

Description

extract the DNA model parameters

Usage

1
2
3
getModelParameters_DNA(obj, features = NULL, full = TRUE)

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

Arguments

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)

Value

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')

Examples

1
2
3
4
5
6
7
8
9
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)

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