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Last data update: 2014.03.03

R: Obtain significant gene-SNP pairs based on a predetermined...

jaguar_process

R Documentation

Obtain significant gene-SNP pairs based on a predetermined threshold value

Description

Function that processes results from running a genome-wide analysis of jaguar and outputs gene-SNP pairs deemed significant by using a predetermined threshold value. It also has an option to print QQ-plot of the p-values from the analysis.

Usage

jaguar_process(jaguar.out,threshold,plot=FALSE)

Arguments

`jaguar.out`	A Matrix of joint score test p-values with genes on rows and SNPs on columns
`threshold`	An numeric value representing a threshold value to call for significance
`plot`	Takes a Boolean value. If 'TRUE', prints a QQ-plot of the p-values from the analysis. In the interests of time and memory management, if there are more than 500,000 gene-SNP pairs in the analysis, only randomly selected 500,000 gene-SNP pairs will be plotted

Value

A matrix containing three columns – 1) Genes, 2) SNPs and 3) P-value from the joint score test approach

Author(s)

Chaitanya R. Acharya, Andrew S. Allen Maintainer: Chaitanya Acharya<c.acharya@duke.edu>

References

Chaitanya R. Acharya, Kouros Owzar, Janice M. McCarthy and Andrew S. Allen; Exploiting expression patterns across multiple tissues to map expression quantitative trait loci (Manuscript submitted)

Chaitanya R. Acharya and Andrew S. Allen; JAGUAR: An R-package to Implement Joint Analysis of Genotype and Group-Specific Variability Using a Novel Score Test to Map eQTL (Manuscript submitted)

Examples

## Example
# 
# Load the example data
data(jaguar_example);

# Genome-wide analysis
Gene_Mat = as.matrix(jaguar_example$GENE_EXP[1:10,])
Geno_Mat = as.matrix(jaguar_example$GENO_MAT)
jag.out = jaguar_gwa(Gene_Mat,Geno_Mat);
dim(jag.out);

# Process results based on a predetermined threshold
result = jaguar_process(jag.out,0.05);
dim(result);

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(JAGUAR)
Loading required package: Rcpp
Loading required package: plyr
Loading required package: lme4
Loading required package: Matrix
Loading required package: reshape2
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/JAGUAR/jaguar_process.Rd_%03d_medium.png", width=480, height=480)
> ### Name: jaguar_process
> ### Title: Obtain significant gene-SNP pairs based on a predetermined
> ###   threshold value
> ### Aliases: jaguar_process
> ### Keywords: score test GWAS eQTL
> 
> ### ** Examples
> 
> ## Example
> # 
> # Load the example data
> data(jaguar_example);
> 
> # Genome-wide analysis
> Gene_Mat = as.matrix(jaguar_example$GENE_EXP[1:10,])
> Geno_Mat = as.matrix(jaguar_example$GENO_MAT)
> jag.out = jaguar_gwa(Gene_Mat,Geno_Mat);

Running Genome-Wide eQTL analysis on  10  genes and  1036  SNPs 

0% 10   20   30   40   50   60   70   80   90   100%
|----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
> dim(jag.out);
[1]   10 1036
> 
> # Process results based on a predetermined threshold
> result = jaguar_process(jag.out,0.05);

Processing JAGUAR results

> dim(result);
[1] 602   3
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>