[GenABEL-dev] GenABEL 1.6-6

[Yurii Aulchenko]

Nicola, Xia,

With upcoming LUPA workshop, I want to release version 1.6-6 of
GenABEL, which include your code changes as well. After release is on
CRAN, and testing at the workshop, it will be announced on forum and
web-site; I will discuss the text of announcement with you.

Please let me know if this is OK with you, and if there are any
last-minute considerations.

CANGES.LOG below; this will serve as the base for announcement.

best wishes,
Yurii


Added Xia Shen's procedure 'polygenic_hglm'. Features: quick
convergence, standard errors for fixed effects.

Updated check.marker, added warning if no. Y-markers is < 10

Applied the patch of Nicola Pirastu
http://lists.r-forge.r-project.org/pipermail/genabel-devel/2011-March/000182.html
to descriptives.trait. Added RUnit regression tests, updated
documentation. Bugs fixed: [#1184], [#1185], [#1259]

Added 'reconstructNPs' function; added extra options
to 'findRelatives'.

Added a number of functions facilitating relationship checks.
The core function is 'findRelatives'. Compared
to guessing relations from genomic kinship matrix, this
procedure offers several enhancements: (1) by use of IBD/IBS
3-state space, it allows to distinguish between some pairs,
which have the same kinship (e.g. parent-offspring from
brother-sister; uncle-nephew from grandparent-grandchild, etc.)
(2) it reports likelihood, allowing for more rigorous inferences

Changes in convert.snp.mach documentation to reflect the fact that
the map-file should have header; changes to convert.snp.illumina
documentation to reflect the nature of the data better; added
option 'mapHasHeaderLine' to convert.snp.ped and updated documentation
(resolving feature request #1317).