mxeqtl: Matrix eQTL function

In shilab/meQTL_functions: What the package does (short line)

Description

Functionalized version of Matrix eQTL

Usage

mxeqtl(snp_file, snp_location, expr_file, expr_location, 
cis_output_file, cis_pval, covariates = "", trans_output_file = "",
trans_pval = 0, model = "linear", MAF = 0, cis_dist = 1e+06,
missing="NA")

Arguments

snp_file	File that contains the genotype data. Required.
snp_location	File that contains genotype genetic locations. Required.
expr_file	File that contains the expression data. Required.
expr_location	File that contains expression location data. Required.
cis_output_file	Name of file cis eQTLs will be output to. Required.
cis_pval	P-value cutoff for cis eQTLs. Required.
covariates	File containing covariate data. Optional.
trans_output_file	Name of file trans eQTLs will be output to. Optional.
trans_pval	P-value cutoff for trans eQTLs. Optional.
model	Model used for analysis. Default is modelLINEAR. Can be set to modelANOVA and modelLINEAR_CROSS. Optional.
MAF	MAF value for filtering. Optional.
cis_dist	Maximum distance for cis eQTLs. Default is 1 megabase (1e6 pb).
missing	String for missing data. Default is NA.

Details

Optional arguments need to be called with their name.

Note

Based off the example code of Andrey A. Shabalin.

Author(s)

Andrew Quitadamo

shilab/meQTL_functions documentation built on May 29, 2019, 9:25 p.m.