setDepthFactors: Manually set library depth correction factors

In MPRAnalyze: Statistical Analysis of MPRA data

Description

Manually set library depth correction factors

Usage

setDepthFactors(obj, dnaDepth, rnaDepth)

Arguments

obj	the MpraObject
dnaDepth	library size factors for the DNA data, a numeric vector of length of the number of columns in the DNA data matrix
rnaDepth	library size factors for the RNA data, a numeric vector of length of the number of columns in the RNA data matrix

Value

the MpraObject with library depth factors

Examples

data <- simulateMPRA(tr = rep(2,10), da=NULL, nbatch=2, nbc=20)
obj <- MpraObject(dnaCounts = data$obs.dna, 
                  rnaCounts = data$obs.rna, 
                  colAnnot = data$annot)
## set constant depth factors (no depth correction)
obj <- setDepthFactors(obj, dnaDepth = rep(1, NCOL(data$obs.dna)),
                              rnaDepth = rep(1, NCOL(data$obs.rna)))

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