getAlpha {MPRAnalyze} | R Documentation |
return the fitted value for the transcription rate.
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")