eqtlTests.me {GGtools} | R Documentation |
use MatrixEQTL computations and statistics as a back end to GGtools eqtlTests
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())
smlSet |
instance of |
rhs |
formula for adjustment of tests for covariates or stratification,
see |
runname |
tag used to distinguish emitted files |
targdir |
folder where ff archives will reside |
pvot |
setting for |
geneApply |
lapply-like function for iteration over genes,
|
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 |
scoretx |
function to be applied to MatrixEQTL statistics. Defaults to abs, for signless association testing |
matrixEQTL.engine.control |
list of parameters passed to |
snpSlicedData.control |
list of parameters used to define |
geneSlicedData.control |
list of parameters used to define |
covarSlicedData.control |
list of parameters used to define |
covariates_file_name |
if covariates are to be used with MatrixEQTL testing engine, they
reside in this file. |
provisional interface
see eqtlTests
intended for simple comparisons
Shabalin et al Bioinformatics (OUP) 2012
if (require(MatrixEQTL)) { g22 = nsFilter( chrFilter( getSS("GGdata", "22"), "22" ), var.cutoff = .8 ) m22 = eqtlTests.me(g22) }