trans.qtl: transQTL interface

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

Description

Interface to the MatrixEQTL Matrix_eQTL_engine() This is a simplified version for more general (trans)QTL analyses, e.g. GWAS or metaboliteQTL and does not need gene annotations

Usage

trans.qtl(prefix, genotype_file_name, vcf = FALSE, snp.pos = NULL,
  expression_file_name, covariates_file_name = character(),
  threshold = 1e-05, compute.all = FALSE, what = NULL,
  min.pv.by.genesnp = FALSE, save.memory = FALSE, verbose = TRUE,
  redo = TRUE, load.qtls = FALSE, keep.outfile = FALSE,
  id.check = FALSE, gene.position = NULL)

Arguments

prefix	path and prefix for the outputfiles (default NULL)
genotype_file_name	filename of a tab separated file with genotype dosage values (usually between 0 and 2) in a matrix nsnp x nsample
vcf	is the genotype file a vcf file that needs to be converted? (default FALSE)
snp.pos	data.frame with SNP positions to be added to matrixEQTL object in the end. Columns named "snps", "chr", "pos", containing information in that order (default NULL) if vcf=TRUE and snp.pos=TRUE | snp.pos=NULL, information is extracted from vcf file unless save.memory=TRUE. if snp.pos=FALSE, no annotation is added
expression_file_name	filename of a tab separated file with expression values in a matrix ngene x nsample. if expression_file_name is a numeric vector (lenght nsample), matrix (ngene x nsample) or data.frame (ngene x nsample), the expression file is created with the name prefix_gene.txt.
covariates_file_name	filename of a tab separated file with covariate values in a matrix ncovar x nsample to not use any covariates, set covariates_file_name=character() if covariates_file_name is a numeric vector (lenght nsample), matrix (ngene x nsample) or data.frame (ngene x nsample), the covariate file is created with the name prefix_covariates.txt.
threshold	significance threshold for eQTLs (default 1e-5), set to 1 to get all QTLs. threshold set to 1 for compute.all=TRUE
compute.all	MatrixEQTL reports only significant results, if results for all tests are required set this to TRUE (default FALSE)
what	flag to determine if a table or the MatrixEQTL object should be returned (default NULL). If unspecified, a table is returned except either save.memory=TRUE or min.pv.by.genesnp=TRUE, then the MatrixEQTL result object is returned.
min.pv.by.genesnp	option to report the minimal pvalue per SNP and per gene in the MatrixEQTL object (default FALSE). If you want to use this option, make sure to set what="object" to get the results.
save.memory	prevent FDR correction (default FALSE). only functional in the github-version of MatrixEQTL, see also https://github.com/andreyshabalin/MatrixEQTL/issues/8
verbose	print comments of progress (default TRUE)
redo	logical, if TRUE the results will always be recomputed, if FALSE the results will be loaded if they exist (default TRUE)
load.qtls	(default FALSE) only relevant for save.memory=TRUE which is mostly used for big datasets. In that case, QTL results are not reported in the MatrixEQTL object but can be read in with load.qtls=TRUE.
keep.outfile	unless compute.all=T or save.memory=T, results are written to a temp file that is deleted. (default FALSE) Parameters /options I would like to add:
id.check	check if ids and order of ids match in genotype, expression and covariate data (default FALSE)
gene.position	data.frame with gene positions in the first 4 columns named "gene_id", "chrom", "start", "end"
threshold.trans	Parameters/options in the old wrapper that do not work currently:

Value

if what="table", the data.frame contained in the MatrixEQTL object me$all$eqtls is returned. If what="object", the whole MatrixEQTL object is returned.

Author(s)

Ines Assum (2019-03-21)

See Also

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

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