jaguar_gwa: Perform genome-wide analysis

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

Description

Computes p-value from our joint score test in a cis framework to map group-specific expression quantitative trait loci (eQTL) that tests for the shifts in gene expression patterns due to genotype and variability among tissues in a mixed effects model framework. A gene-level p-value is computed using a permutation-resampling scheme in order to investigate if a gene has at least one eQTL across all the groups.

Usage

jaguar_gwa(geneexp,genomat,write=FALSE)

Arguments

geneexp	A matrix of gene expression data with gene on rows and patient samples on columns. There has to be equal number of samples in each group. Samples (columns in the geneexp object) with missing gene expression values for any group/tissue MUST be included in the data
genomat	A matrix of genotype data recoded as single allele dosage number (i.e. 0, 1 or 2) with rows representing SNPs and columns representing samples
write	Boolean value indicating whether the results should be outputted into a tab-delimited text file. The default value is FALSE.

Value

A matrix of raw unadjusted p-values with rows representing genes and columns representing SNPs

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_process,jaguar_slice,jaguar_sim,jaguar_cis,jaguar_plotqtl

Examples

# Load the example data
data(jaguar_example);

# Run a cis analysis with no permutations
Gene_Mat = as.matrix(jaguar_example$GENE_EXP[1:10,])
Geno_Mat = as.matrix(jaguar_example$GENO_MAT)
out = jaguar_gwa(Gene_Mat,Geno_Mat);
dim(out)

cramanuj/JAGUAR documentation built on May 13, 2019, 10:55 p.m.