summary: Summary of comparison results.

In lunge111/intSEQ: Differential Expression Analysis of RNA-seq Data with Integrated Likelihood Method

Description

Show the simulation results of simuComp for limma voom, limma trans, integrated likelihood and Quasi likelihood method.

Usage

## S3 method for class 'intcomp'
summary(intcomp, difflevel = c("all", "small", "medium", "large"), ...)

Arguments

intcomp	A object returned by simuComp.
difflevel	Which subgroup of genes is shown.
...	Other arguments that are currently not used.

Details

If the intcomp was produced under null = TRUE. A table of empirical false positive rate (the number of rejections divided by the number of outcomes, since the simulations are all under null condition, all rejections are false positives) will be displayed.

If the intcomp was produced under null = FALSE. First, the discovery rates (the number of rejections divided by the number of outcomes) under fdrlevel in simuComp will be presented for the four methods. Then a table of discovery rate under p values thresholds defined by levels in simuComp will be displayed.

Author(s)

Yilun Zhang, David Rocke

Examples

## Not run: 
data(count.data)
data(condition)
count=count.data[,1:10]
cond=rep(0:1,each=5)
res=intSEQ(count, cond)
simu.res <- simuComp(res, ntime = 2)
summary(simu.res, difflevel="all")
summary(simu.res, difflevel="small")
summary(simu.res, difflevel="medium")
summary(simu.res, difflevel="large")

## End(Not run)

lunge111/intSEQ documentation built on May 20, 2019, 9:38 a.m.