eqtlTests.me: use MatrixEQTL computations and statistics as a back end to...

In GGtools: software and data for analyses in genetics of gene expression

Description

use MatrixEQTL computations and statistics as a back end to GGtools eqtlTests

Usage

eqtlTests.me(smlSet, rhs = ~1, runname = "20", 
  targdir = "cisScratch.me", pvot = 0.5, geneApply = lapply, 
  shortfac = 100, checkValid = TRUE, useUncertain = TRUE, 
  glmfamily = "gaussian", scoretx = abs, 
  matrixEQTL.engine.control = 
    list(output_file_name = "/dev/null",
    useModel = modelLINEAR, 
    errorCovariance = numeric(), 
    verbose = FALSE, 
    pvalue.hist = FALSE), 
  snpSlicedData.control = .slicedDataDefaults, 
  geneSlicedData.control = .slicedDataDefaults, 
  covarSlicedData.control = .slicedDataDefaults, 
  covariates_file_name = character())

Arguments

smlSet	instance of smlSet-class
rhs	formula for adjustment of tests for covariates or stratification, see snp.rhs.tests
runname	tag used to distinguish emitted files
targdir	folder where ff archives will reside
pvot	setting for pvOutputThreshold in Matrix_eQTL_engine
geneApply	lapply-like function for iteration over genes, mclapply is suitable when in multicore environments
shortfac	scaling factor to increase precision when test results are stored as short ints in ff
checkValid	logical to check validity of input smlSet
useUncertain	logical informing snp.rhs.tests that imputed real-valued B allele counts may be present among genotype data
glmfamily	family specification for snp.rhs.tests
scoretx	function to be applied to MatrixEQTL statistics. Defaults to abs, for signless association testing
matrixEQTL.engine.control	list of parameters passed to Matrix_eQTL_engine
snpSlicedData.control	list of parameters used to define SlicedData-class instances
geneSlicedData.control	list of parameters used to define SlicedData-class instances
covarSlicedData.control	list of parameters used to define SlicedData-class instances
covariates_file_name	if covariates are to be used with MatrixEQTL testing engine, they reside in this file. regressOut can be used to avoid this if plug-in FDR are to be used

Details

provisional interface

Value

see eqtlTests

Note

intended for simple comparisons

References

Shabalin et al Bioinformatics (OUP) 2012

Examples

if (require(MatrixEQTL)) {
 g22 = nsFilter( chrFilter( getSS("GGdata", "22"), "22" ), var.cutoff = .8 )
 m22 = eqtlTests.me(g22)
}

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.