R/qtl version 1.08-55

[Karl Broman]

A new version of R/qtl (1.08-55) has been released at its web site
(http://www.rqtl.org). The Windows and Mac binaries should be
available within a few days.

See http://www.rqtl.org/STATUS.txt for a list of changes. The major
changes are listed below; they are quite extensive.

We have added several new functions for exploring multiple QTL models.
The syntax for the fitqtl function has changed slightly, to give
consistency among various multiple-QTL functions

A document describing the use of the new functions is available at
http://www.rqtl.org/tutorials/new_multiqtl.pdf

We have done our best to test and debug the new code, but because of
the extensive changes, we fear that some bugs remain, so please view
results skeptically and let us know of any potential problems.

As always, I'd appreciate hearing any suggestions or comments or
complaints.

Karl Broman
kbr...@biostat.wisc.edu

------

Major changes:

For all functions taking a "pheno.col" argument (including scanone
and scantwo), this argument can now be a character string indicating
the name of a phenotype. (Previously, it had to be a numeric index
indicating the phenotype).

fitqtl now takes a cross object and pheno.col (as with scanone,
scantwo and scanqtl), rather than a column of phenotypes.

Implemented Haley-Knott regression for the fit of multiple-QTL
models in fitqtl and scanqtl.

Added functions addint, addqtl, and addpair, for exploration of
multiple QTL models. addint tries adding all possible pairwise
interactions, one at a time, to a multiple QTL model. addqtl scans
for an additional QTL to be added to a multiple QTL model. addpair
scans for an additional pair of QTL to be added to a multiple QTL
model.

Added functions addtoqtl, dropfromqtl, and replaceqtl, for
manipulating a qtl object created by makeqtl().

Added a function refineqtl(), for getting the maximum likelihood
estimates of QTL positons (as best we can) in the context of a
multiple-QTL model. Added a function plotLodProfile which can
create a figure with 1-dimensional LOD profiles for each QTL, in the
context of a multiple QTL model, as is commonly created for multiple
interval mapping.

Added a function, tryallpositions(), for testing all possible
positions for a given marker, keeping the order of all other markers
fixed.

Added a function, compareorder(), for comparing a given order of
markers on a single chromosome to the current one contained within a
cross object.

Added some additional marker genotype codes for the phase-known
4-way cross, for a dominant marker with both parents being
heterozygous: 11 = not AC, 12 = not BC, 13 = not AD, 14 = not BD.

Revised est.rf, for estimating recombination fractions between all
pairs of markers, so that it can give results for many of the
incompletely informative markers in a 4-way cross.