QRank (version 1.0)

QRank-package: A Novel Quantile Regression Tool for eQTL discovery

Description

A Quantile Rank-score (QRank) based test for the identification of expression quantitative trait loci (eQTLs).

Details

We use a Quantile Rank-score (QRank) based test to identify the expression quantitative trait loci (eQTLs) that are associated with the conditional quantile function of gene expressions.

References

Xiaoyu Song, Gen Li, Zhenwei Zhou, Xianling Wang, Iuliana Ionita-Laza and Ying Wei (2016). QRank: A Novel Quantile Regression Tool for eQTL Discovery. Under revision for Bioinformatics.

Examples

set.seed(123)                                                                        #
n=300                                                                                #
x=rbinom(n, 2, 0.2)                                                                  #
y=rnorm(n, mean=0, sd=1)                                                             #
z=cbind(rbinom(n, 1, 0.3), rnorm(n, mean=2, sd=2))                                   # 
taus=c( 0.25, 0.5, 0.75)                                                             # 

# - run the proposed QRank approach                                                  #
QRank(gene=y, snp=x, cov=z, tau=taus)                                                #

# - output                                                                           #
#Composite.pvalue:                                                                   #
#[1] 0.2241873                                                                       #

#Quantile.specific.pvalue:                                                           #
#    0.25       0.5      0.75                                                        #
#0.5452044 0.1821452 0.5938421                                                       #