knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
doseLM is a testing platform for dosage compensation analyses using established differential sequencing analysis tools, including edgeR.
Once installed, you must load the package.
library(edgeR) library(doseLM) library(doseR) library(SummarizedExperiment)
#par(mfrow=c(1,5)) type1 <- simData() ; # you get sig result for the comparison between just MF and just AZ type2 <- simData(FZ=1, MZ=1) ; #you get sig result for comparison between just MF and all the other 3 type3 <- simData(MZ=1) ; # you get sig result for all comparisons except: justMF and MF+AZ, just MF and just AZ type4 <- simData(FZ=100) ; # interaction effect, secondd one sig (same as type 3) type5 <- simData(FA= 100, FZ=100) ; #you get sig result for all comparisons except: justMF and MF+AZ, just MF and just AZ
d1(type1) d1(type2) d1(type3) d1(type4) d1(type5)
d0(type1) d0(type2) d0(type3) d0(type4) d0(type5)
Results from d0
type2 , clearly A biased type3 clearly Z
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