Description Usage Arguments Value Author(s) See Also
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
1 2 3 4 5 6 | 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)
|
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: |
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.
Ines Assum (2019-03-21)
Other eqtl functions: eqtl.min.p
,
eqtl.run
, eqtl
,
myWaitForJobs
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