getFits_DNA {MPRAnalyze}R Documentation

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.

Description

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.

Usage

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

Arguments

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.

Value

DNA fits (numeric, enhancers x samples)

Examples

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)

[Package MPRAnalyze version 1.11.0 Index]