Description Usage Arguments Value Author(s) References See Also Examples
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.
1 | jaguar_process(jaguar.out,threshold,plot=FALSE)
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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 |
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A matrix containing three columns – 1) Genes, 2) SNPs and 3) P-value from the joint score test approach |
Chaitanya R. Acharya Maintainer: Chaitanya Acharya<c.acharya@duke.edu>
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
jaguar_gwa,jaguar_slice,jaguar_sim,jaguar_plotqtl,jaguar_cis
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## 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);
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