getFits_RNA: Get RNA model-based estimates from an MpraObject (the...

Description Usage Arguments Value Examples

View source: R/accessFunctions.R

Description

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.

Usage

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getFits_RNA(obj, enhancers = NULL, depth = TRUE, full = TRUE,
  rnascale = TRUE)

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.

rnascale

if controls were used to correct the fitting (in comparative analyses), use these factors to re-adjust the estimates back.

Value

RNA fits (numeric, enhancers x samples)

Examples

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data <- simulateMPRA(tr = rep(2,5), da=NULL, 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)

MPRAnalyze documentation built on Nov. 8, 2020, 8:22 p.m.