README.md

In SharonLutz/powerASEeQTL: This package runs a power analysis on RNAseq data

powerASEeQTL

The powerASEeQTL R package runs power calculations for allele specific expression (ASE) and eQTL analysis using RNA-seq data and creates plots of these results.

Installation

install.packages("devtools") # devtools must be installed first
install.packages("MASS") #this package must be installed first
install.packages("VGAM") #this package must be installed first

devtools::install_github("SharonLutz/powerASEeQTL")

Example

The code below creates a plot of the power calculations for the eQTL and ASE analyses for RNA-seq data with the following parameters:

library(powerASEeQTL)

#case 1: methods for eQTL and ASE (faster)
powerASEeQTL(n = 500, mu = 500, n.simu = 500,methods=c("eQTL.linear","eQTL.negBin","eQTL.quasipoisson","ASE"),
folds = seq(1.5, 2, by = 0.25),alpha = 0.001, phi = 1.1, theta = 0.1, maf = 0.2, sim = "sim1")

#case 2: all methods (slower)
powerASEeQTL(n = 500, mu = 500, n.simu = 500,methods=c("eQTL.linear","eQTL.negBin","eQTL.quasipoisson","ASE", "eQTL.ASE"),
folds = seq(1.5, 2, by = 0.25),alpha = 0.001, phi = 1.1, theta = 0.1, maf = 0.2, sim = "sim1")

Output

For this analysis, we get the following plot where the y-axis is power and the x-axis is the fold change.

Reference

Power Calculations for eQTL Mapping and Allele Specific Expression with RNA-seq Data. (Submitted)

SharonLutz/powerASEeQTL documentation built on Nov. 12, 2020, 11:15 a.m.