eqtlTests.me {GGtools} | R Documentation

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

### 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)
    }

[Package GGtools version 5.25.3 Index]