In scantwoF.R: when pheno.cols is a single number, subsetting the cross object with it to get pheno returns a vector, not a data frame.
This results in subsetting errors later when using pheno. pheno now gets coerced into a data frame.

In stepwiseqtlF.R: similarly, when pheno.cols is a single number, only one set of residuals gets returned in the lm calls. These residuals
are stored in a numeric vector, not a matrix, so colSums gives an error. Now coerces the residuals into a matrix before calling colSums.