getFits_RNA {MPRAnalyze} | R Documentation |
Get RNA 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_RNA(obj, enhancers = NULL, depth = TRUE, full = TRUE, rnascale = TRUE)
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. |
rnascale |
if controls were used to correct the fitting (in comparative analyses), use these factors to re-adjust the estimates back. |
RNA 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) rna.fits <- getFits_RNA(obj)