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

If you any additions or revisions to suggest, please send an email to
Karl Broman, <kbroman@jhsph.edu>.
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SHORT TERM:

o effectscan: if one chromosome, plot map positions on the x-axis 
  rather than the chromosome ID

o Modify a.starting.point and the tutorial to discuss the new version
  of plot.scantwo.

o Update the tutorial, especially regarding the X chromosome and the
  makeqtl/fitqtl/scanqtl.

o read.cross tests within package

o Map positions in QTX format data for the function read.cross.

o Need to modify the map expansion for RI lines for the X chromosome.

o Add appropriate functions to analyze advanced intercrosses (AILs). 

o Documentation on RI lines.

o Deal with the X chromosome appropriately in scanone, scantwo,
  fitqtl, makeqtl and scanqtl.

o Add an example regarding the X chromosome to the help files for
  fake.f2 and scanone.

o Rescale LOD score for X chromosome in scanone/two? 


MEDIUM TERM:

o Coefficient estimates by imputation in fitqtl.

o MIM for a set of QTLs at specified locations with specified
  interactions (as a new method in fitqtl and scanqtl).

o refineqtl -- like fitqtl, but refines the locations of the QTLs as
  in Zhao-Bang's MIM

o Deal with the X chromosome appropriately in scantwo with method="em"

o max.scanqtl, summary.scanqtl, print.summary.scanqtl, plot.scanqtl

o Modify plot.rf and plot.errorlod to allow plot of a color scale, as
  in plot.scantwo.  

o In MIM: allow return of SEs of effects.  Write coef.mim, resid.mim,
  and dev.mim to pull out the est'd coefficients, the residuals, and
  the "deviance" (2 * ln likelihood).

o In MIM, refinement of QTL location and plots of that.

o calc.genoprob and sim.geno for "f2ss" (intercross with sex-specific
  maps) 


LONG TERM:

o Composite interval mapping, in an automated way.

o Imprinting/parent-of-origin effects.

o Treating a covariate as a random effect.

o Multiple phenotypes (esp. regarding pleiotropy).

o Data conversion functions to/from Chuck Berry's bqtl package

o subset.scanone, subset.scantwo

o Model search for MIM etc.

o Function to plot, for a specified q1, LOD{q2|q1} vs q2 (using the
  output from scantwo).

o Take the fit of the null model outside of the C code for
  the imputation method in scanone and scantwo, so that it
  only has to be done once (rather than for each chr or chr pair).

o Starting values for EM for the two-part model (and more generally).
  Allow the option of an automatic selection of multiple starting
  points. 

o Generalized linear models in scanone and scantwo.

o Analysis functions such as scanone and scantwo might assign an
  attribute to their output which identifies the input data and/or
  function call.

o Re-write the C code for EM underneath scanone and scantwo so that it
  is not so tedious.

o Wrappers for Brian Yandell's bmapqtl software to do QTL mapping by
  MCMC. 

o Individual numbers in plot.geno function; allow it to plot only
  individuals with apparent genotyping errors, with a mix of
  chromosomes. 

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end of TODO.txt
