[GenABEL-dev] GenABEL 1.6-6

[Xia Shen]

Quite OK :)

Xia

On May 2, 2011, at 12:59 PM, Yurii Aulchenko wrote:

> 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).