runMatrixEQTL: A wrapper around MatrixeQTL
In kauralasoo/seqUtils:

Description Usage Arguments Value Author(s)

Prepares SlicedData objects of expression data, genotypes and covariates and then runs MatrixeQTL on the data.

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runMatrixEQTL(exp_data, geno_data, snpspos, genepos, covariates = NULL,
  cisDist = 5e+05, pvOutputThreshold = 0.01, permute = FALSE,
  model = modelLINEAR)

`exp_data`	Matrix of gene expression data (genes in rows, samples in columns).
`geno_data`	Matrix of genotype data (SNPs in rows, samples in columns).
`snpspos`	Matrix of SNP coordinates (columns: snpid,chr,pos).
`genepos`	Matrix of gene coordinates (columns: geneid,chr,left,right).
`covariates`	Matrix of covariates (samples in columns).
`cisDist`	cis distance from the gene.
`pvOutputThreshold`	Maximum p-value to report. Smaller values make the code quicker.
`permute`	Permute genotype labels before qtl mapping.
`model`	Specifies which MatrixEQTL model to use. Options: modelLINEAR, modelLINEAR_CROSS and modelANOVA.