getAlpha: return the fitted value for the transcription rate.
In YosefLab/MPRAnalyze: Statistical Analysis of MPRA data

Description Usage Arguments Value Examples

return the fitted value for the transcription rate.

1	getAlpha(obj, by.factor = NULL, full = TRUE)

`obj`	the MpraObject to extract from, must be after model fitting
`by.factor`	return a matrix of values, corresponding to the estimated rates of transcription under different values of a factor included in the design. Value must be of these options: NULL: (default) return only the intercept term, a single baseline rate for each enhancer "all": will return the corresponding transcription rates for all values included in the model factor name: must be a factor included in the RNA annotations and the rna design. Will return the corresponding rates for all values of the given factor
`full`	if true, return rate of the full model (default), otherwise of the reduced model (only applies if an LRT-based analysis was used)

the estimate for transcription rate as fitted by the model

data <- simulateMPRA(tr = rep(2,10), da=c(rep(0,5), rep(1,5)), 
                     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 <- analyzeComparative(obj, dnaDesign = ~ batch + barcode + condition, 
                              rnaDesign = ~ condition, reducedDesign = ~ 1)
## get alpha estimate for the two conditions
alpha <- getAlpha(obj, by.factor="condition")