[no description] https://git.osdyson.ru/mirror/pkgsrc/atom?h=pkgsrc_2011Q4 2008-10-14T07:38:26Z 2008-10-14T07:38:26Z markd markd 2008-10-14T07:38:26Z urn:sha1:395629bf09d8da222d3d245b68a04a79a62dd839 genetics 1.3.4 - 2008-08-20 --------------------------- - Fix bug in makeGenotypes that caused it to ignore the 'sep' argument when determining which columns contain genotypes & add a corresponing regression test genetics 1.3.3 - 2007-04-29 --------------------------- - Correct 'obsolete' use of '$'. R no longer permits '$' to be used to extract named elements from vectors (just lists). - Remove the power.casectl() function, which was based on invalid assumpations. It has been marked depreciated. Please use the functions in the Bioconductor package 'GeneticsDesign' instead. genetics 1.3.2 - 2007-11-20 --------------------------- - Fix bug in handling of assignment of NA value(s) to elements of an existing genotype object. - Fix warning messages from R CMD CHECK - Correct documentation error by swapping definitions of kp and alpha arguments of power.casectl(). genetics 1.3.1 -------------- - fixes in genotypeOrder to ensure all genotype/haplotype combinations are used. - genotypeOrder<- is now exported genetics 1.3.0 -------------- - A note is now displayed on startup: The R-Genetics project has developed an set of enhanced genetics packages that will shortly replace 'genetics'. Please visit the project homepage at http://rgenetics.org for more information. - binsearch() has been moved to the gtools package - New function groupGenotype to create groups/levels based on genotype names - Added some internal utility functions (.genotype2Haplotype, .genotype2Allele, and .matchGenotype) - Genotype class gets additional slot genotypeOrder (and genotype() function gets additional argument with the same name) in order to enable predefined order of genotypes in other functions e.g. summary - Added order, sort and %in% methods for genotype and haplotype classes. - Fixed genotype() with allow.partial.missing=FALSE when 'alleles' argument is passed - There is no more warning in genotype() if 'a1' or 'a2' have NA value(s) and 'alleles'' argument is specified, since NA is NA anyway - Fixed documentation of power.casectrl() - added gtools to Depends as needed by expectedGenotypes(); the latter now gives sorted genotypes according to order of given alleles - print.HWE.test() wasn't displaying the observed vs expected genotype frequency table. Fixed. genetics 1.2.1 -------------- - Update Greg's email address - Fixed a bug in function allele.number, as pointed out by Chris Wallace 2007-10-25T16:54:26Z jlam jlam 2007-10-25T16:54:26Z urn:sha1:5e1040eb4b3d5bdf7e0d465818a3ff084620adb3 can handle packages having no PLIST files. 2006-07-02T13:19:53Z markd markd 2006-07-02T13:19:53Z urn:sha1:2961d8886714393e1988eeba200b6a8f72c00612 Fixes build problem seen in bulk builds. 2006-02-05T23:08:03Z joerg joerg 2006-02-05T23:08:03Z urn:sha1:93e3b9e04264b93620166058e19ea42c856505b0 2005-11-04T08:13:15Z rillig rillig 2005-11-04T08:13:15Z urn:sha1:167a756b9060641832ff9c4e5968414554b13f65 Classes and methods for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium, ...