Description Usage Arguments Value Examples
View source: R/analysisFunctions.R
epirical: the model is fitted as specified, enabling future empirical testing (either empirical p-value if negative controls are provided, or a global devience analysis, see details in 'test.empirical')
lrt: only available if negative controls are provided. A likelihood ratio test is used, with the null hypothesis a joint model of the controls and a given candidate sequence, and the alternative model being a separate model for controls and candidates.
1 | analyzeQuantification(obj, dnaDesign = ~1, rnaDesign = ~1)
|
obj |
the MpraObject |
dnaDesign |
the design of the DNA counts |
rnaDesign |
the design of the RNA counts |
the MpraObject, with populated models
1 2 3 4 5 6 7 | 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)
|
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