| Type: | Package |
| Title: | A Novel Quantile Regression Approach for eQTL Discovery |
| Version: | 1.0 |
| Date: | 2016-12-25 |
| Author: | Xiaoyu Song |
| Maintainer: | Xiaoyu Song <xs2148@cumc.columbia.edu> |
| Description: | A Quantile Rank-score based test for the identification of expression quantitative trait loci. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Imports: | quantreg |
| NeedsCompilation: | no |
| Packaged: | 2017-01-11 17:13:44 UTC; Destiny |
| Repository: | CRAN |
| Date/Publication: | 2017-01-11 18:47:57 |
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.
Author(s)
Xiaoyu Song
Maintainer: Xiaoyu Song <xs2148@cumc.columbia.edu>
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 #
A new Quantile Rank-score (QRank) based test for the eQTL identification.
Description
A function to obtain the p-value on the association between a gene expression and a genetic variant based on quantile rank-score test.
Usage
QRank(gene, snp, cov = NULL, tau)
Arguments
gene |
a gene expression level from a selected gene. No parametric assumption is needed for underlying distribution. |
snp |
a selected SNP. |
cov |
a vector or matrix of covariates. Default is NULL. |
tau |
the quantile levels to be estimated. Tau can be a single value or a vector of quantile levels. |
Details
This function conducts Quantile Rank-score (QRank) based test for the continuous traits. It can be used to identify expression quantitative trait loci (eQTLs) that are associated with the conditional quantile functions of gene expression.
Value
composite.pvalue |
a single p-value for across all quantile levels under consideration, testing H0: No genetic association at the selected quantile levels. |
quantile.specific.pvalue |
p-values of each quantile level, testing |
Author(s)
Xiaoyu Song
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 #
Heterogeneity index for "QRank"
Description
Calculate the heterogeneity index of quantile regression coefficients at multiple quantile levels. It measures the variation of the quantile coefficients across quantile levels.
heterogeneity=log(sd(\beta)/abs(mean(\beta)))
where \beta is the vector of quantile regression coefficients at multiple quantile levels.
Usage
heter.QRank(object, newtaus=NULL)
Arguments
object |
Object returned from "QRank" |
newtaus |
a vector of quantile levels based on which heterogeneity index are calculated. Default is NULL, in which case the quantile levels inherited from "QRank" will be used. |
Value
heterogeneity index |
one hetergeneity index |
See Also
Examples
# continuted from "QRank"
taus=c( 0.25, 0.5, 0.75)
q = QRank(gene=y, snp=x, cov=z, tau=taus)
heter.QRank(q) # default uses taus inherited from "QRank"
# - output
#Heterogeneity index:
#[1] 2.474184
heter.QRank(q,newtaus = 1:9/10) # calculate based on new taus values
# - output
#Heterogeneity index:
#[1] 2.69242
Print a QRank object
Description
Print the object of QRank
Usage
## S3 method for class 'QRank'
print(x, ...)
Arguments
x |
Object returned from QRank. |
... |
Optional arguments |
See Also
Print a QRank.heter object
Description
Print the object of heter.QRank
Usage
## S3 method for class 'QRank.heter'
print(x, ...)
Arguments
x |
Object returned from heter.QRank. |
... |
Optional arguments |