Bug with GxE when using GenotypeIterator

[jonaszierer]

In assocTestSingle for GenotypeIterator it iterates over the SNP blocks. In each iteration GxE (the name of ithe interaction effects) is set to the model matrix.

if (!is.null(GxE)) GxE <- .modelMatrixColumns(null.model, GxE)

That works in the fist iteration when GxE is still a character but fails in the second iteration where GxE is already a model matrix. This should probably be moved outside the loop or changed to

if (!is.null(GxE)) GxE_m <- .modelMatrixColumns(null.model, GxE) 
assoc <- GENESIS:::testGenoSingleVar(null.model, G=geno, E=GxE_m, test=test)

(Though I can't really see a reson not to move it to before the start of the loop)

[smgogarten]

Thanks, fixed in 687ad1c and release v2.14.3