for loop in plotlod changed to loop through uchr, not seq(along=uchr).
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.
Merge branch 'master' of git://github.com/jwliang2/funqtl into jwliang2

Conflicts: R/plotlod.R
  (fixed a problem I'd just fixed, but in a better way)
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