In avastermark19/doseLM: doseLM

knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)

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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)

MF MF MF MF+AZ MF+AZ MF*AZ

MF+AZ MFAZ AZ MFAZ AZ AZ

Type1 1 1 *** 1 1 1

Type2 * * 1 1 1

Type3 1 1

Type4 * 1

Type5 1 * 1 *

#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

avastermark19/doseLM documentation built on May 5, 2019, 7:56 p.m.