jaguar_cis: Perform cis-eQTL 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_cis(geneexp,genomat,snp.bed,gene.bed,cisDist=100000,nperm=10000,seed=100)

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
snp.bed	BED file format of SNP description. For more information, see http://genome.ucsc.edu/FAQ/FAQformat.html#format1 or the example data
gene.bed	BED file format of Gene description. For more information, see http://genome.ucsc.edu/FAQ/FAQformat.html#format1 or the example data
cisDist	cis distance is defined as the maximum absolute distance between the gene and a SNP. Default value is 100Kb
nperm	Number of permutations. Default value is 10,000. Note that if it is 0, no permutations are performed
seed	Seed value for permutations

Value

If permutations are performed, a list object with the following components is returned -

results	A matrix containing gene-level permutation p-values
cisSNPs	A list object containing the cis-SNPs corresponding to the genes in results

If permutations are not performed -

A matrix containing raw unadjusted p-values for all gene-cisSNP pairs

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_gwa,jaguar_plotqtl

Examples

# Load the example data
data(jaguar_example);
Gene = jaguar_example$GENE_EXP
SNP = jaguar_example$GENO_MAT
gene_loc = jaguar_example$GENE_BED
snp_loc = jaguar_example$SNP_BED
# Run a cis analysis with no permutations
out = jaguar_cis(Gene,SNP,snp_loc,gene_loc,nperm=0);
length(out)

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