runMatrixEQTL: A wrapper around MatrixeQTL

Description Usage Arguments Value Author(s)

View source: R/qtl_matrixEQTL.R

Description

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

Usage

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

Arguments

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.

Value

MatrixeQTL result object.

Author(s)

Kaur Alasoo


kauralasoo/seqUtils documentation built on Sept. 24, 2018, 1:11 a.m.