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

In JAGUAR: Joint Analysis of Genotype and Group-Specific Variability Using a Novel Score Test Approach to Map Expression Quantitative Trait Loci (eQTL)

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 Maintainer: Chaitanya Acharya<[e-mail]>

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. BMC Bioinformatics (2016) 17:257 DOI 10.1186/s12859-016-1123-5

See Also

jaguar_gwa,jaguar_slice,jaguar_sim,jaguar_plotqtl,jaguar_cis

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);

JAGUAR documentation built on May 2, 2019, 3:26 p.m.