getFits_DNA: Get DNA model-based estimates from an MpraObject (the...
In YosefLab/MPRAnalyze: Statistical Analysis of MPRA data

Description Usage Arguments Value Examples

Get DNA model-based estimates from an MpraObject (the expected values based on the model). These can be compared with the observed counts to assess goodness of fit.

getFits_DNA(
  obj,
  enhancers = NULL,
  depth = TRUE,
  full = TRUE,
  transition = FALSE
)

`obj`	MpraObject to extract from
`enhancers`	which enhancers to get the fits for. Can be character vectors with enhancer names, logical or numeric enhancer indices, or NULL if all enhancers are to be extracted (default)
`depth`	include depth correction in the model fitting (default TRUE)
`full`	if LRT modeling was used, TRUE (default) would return the fits of the full model, FALSEwould return the reduced model fits.
`transition`	use the DNA->RNA transition matrix (deafult: FALSE). This is useful if the DNA observations need to be distributed to match the RNA observations.

DNA fits (numeric, enhancers x samples)

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)
dna.fits <- getFits_DNA(obj)