eqtl: basic eQTL interface

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

Description

Basic interface to MatrixEQTL passing all data in files

Usage

eqtl(expression_file_name, genotype_file_name, covariates_file_name,
  gene.position, snp.pos, prefix, redo = FALSE, threshold = 1e-05,
  compute.all = FALSE, what = "table")

Arguments

expression_file_name	filename of a tab separated file with expression values in a matrix ngene 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
covariates_file_name	filename of a tab separated file with covariate values in a matrix ncovar 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"
prefix	name prefix for the outputfilenames
redo	logical, if TRUE the results will always be recomputed, if FALSE the results will be loaded if they exist (default FALSE)
threshold	significance threshold for eQTLs (default 1e-5)
compute.all	MatrixEQTL reports only significant results, if results for all tests are required set this to TRUE (default FALSE)
what	flag to determine what should be returned (default "table"). Can be set to "object" to get the MatrixEQTL result object.

Value

if what is "table" the function returns the eQTL results as a table if what is "object" the function returns the MatrixEQTL object.

See Also

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

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