
"To do" list for R/lineup
----------------------------------------------------------------------
This file is intended to contain a list of additions and revisions
that are planned for the R/lineup package.

If you any additions or revisions to suggest, please send an email to
Karl Broman, <kbroman@biostat.wisc.edu>.
----------------------------------------------------------------------

o write a vignette

o Write function like corbetw2mat but within a given matrix, with
  options "bestpairs" or "bestforeach"

o Function for adding the two sets of distance results.  (Say for
  combining the comparisons between genotype and each of multiple
  tissues). 

o Why are there so many eQTL obs/inf mismatches?
  Perhaps weight the eQTL by their proportion of mismatches across all
  mice?

o A function for making those pairs plots for a set of individuals
  from one or two tissues.

o Another plot of distance matrix: image of dichotomized version of
  distance (some threshold as input, checking d.method to decide
  whether to color above or below threshold).

o distep, and distgp, for phenotype data

o algorithm for using distances to make a decision about what is
  messed up (that is, what happened).  I guess separate the inference
  of errors from the correction of errors.

o Include a vignette

----------------------------------------------------------------------
end of TODO.txt
