eqtl.run: basic eQTL interface

In matthiasheinig/eQTLpipeline: A package to facilitate the full pipeline of cis eQTL analysis

Description

Basic interface to MatrixEQTL passing expression and covariate data in matrices, and genotypes as a file uses the eqtl function

Usage

eqtl.run(expr, covar, genotype_file_name, gene.position, snp.pos, id, ...)

Arguments

expr	expression values in a matrix ngene x nsample
covar	covariate values in a matrix ncovar x nsample
genotype_file_name	filename of a tab separated file with genotype dosage values (usually between 0 and 2) in a matrix nsnp x nsample
gene.position	data.frame with gene positions in the first 4 columns named "chrom", "start", "end", "gene_id"
snp.pos	data.frame with SNP positions in the first three columns named "snp_id", "chrom", "snp_pos"
id	character indicating an id used for tempfile creation

Value

the same output as the eqtl function

See Also

Other eqtl functions: eqtl.min.p, eqtl, myWaitForJobs, trans.qtl

matthiasheinig/eQTLpipeline documentation built on May 21, 2019, 1:16 p.m.