genetics 1.3.8 - 2012-12-14 --------------------------- Bug fixes: - Regenerate broken PDF files in inst/doc. genetics 1.3.7 - 2012-09-14 --------------------------- Enhancements: - Improve descripiton of last examples in manual page for HWE.test(). Other Changes: - Correct warnings issued by recent versions of R CMD CHECK. genetics 1.3.6 - 2011-02-01 --------------------------- - Add missing 'locus<-', 'gene<-', and 'marker<-' functions to NAMESPACE file. - Update Greg's email address to greg@warnes.net genetics 1.3.5 - 2011-01-17 --------------------------- - Fix warning messages from R CMD check 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 genetics 1.2.0 ------------- - Add R^2 to HWE and LD estimates - Correct bug in denominator of Heterozygosity calculation, as identified by Christopher Calrson - Fix handling of the 'type' and 'what' arguments for plot.genotype() - Misc bug fixes in package imports/dependencies/etc. - Add expectedGenotypes() and plot.genotypes() contributed by Gregor GORJANC - Fix bug in heterozygote when more than one allele.name is provided - Return NA and issue a warning if diseq() called on a marker with only one observed allele. genetics 1.1.2 -------------- - Remove debugging code that printed intermediate values (sometimes a lot of them). - Ensure that allele.freq table reported by summary.genotype has the same ordering as allele.names table. genetics 1.1.1 -------------- - Make it clear that the Yates continuty correction is applied *only* when simulate.p.value=FALSE, so that the reported test statistics for simulate.p.value=FALSE and simulate.p.value=TRUE will differ. - Attempt to fix/clarify HWE diseq. computations & synchronize documentation. - Updated to use a namespace and to work with the lastest gregmisc bundle, which was previously a package. genetics 1.1.0 -------------- - Add namespace support - R/diseq.R: Restore ability to show Observed vs. Expected table by adding "table" option for the 'show' parameter. - Updates to power.casectrl. (including renaming from power.casectl) - Update to work with gregmisc now that it has been converted from a package to a bundle. genetics 1.0.4 -------------- - Updated to remove warnings in R CMD check for R 1.9.1. genetics 1.0.2 -------------- - Fixed Heterozygosity (H) and PIC calculations in summary.genotype. (Bug report from Gerard Tromp <gtromp@cmb.biosci.wayne.edu>. - Added experimental, undocumented, and untested function hapmcmc for imputing haplotypes and related functions. (Code submitted by David Duffy <davidD@qimr.edu.au>). genetics 1.0.1 -------------- - Fixed mislabeling of rows/columns in LDtable - Extended LDtable to resize text to fit box area, and to allow selection of which statistics are displayed, and which statistic is used for coloration. - Extended LDtable to allow all columns & rows to be shown - Added a larger example to plot.LD.data.frame documentation - Changed the name of some function parameters to be more clear and/or consistent - Added summary.LD.data.frame and print.LD.data.frame - Fixed a bug in genotype() when reorder="no", such as when called by haplotype(). genetics 1.0.0 -------------- - New functions to estimate and test linkage disequilibrium (LD): LD, LD.genotype, LD.data.frame - New functions to display LD results print.LD, print.LD.data.frame, plot.LD.data.frame, LDtable, LDplot - Various bug-fixes and corrections genetics 0.6.8 -------------- - Added HWE.chisq which performs the Chi-Square test for Hardy-Wienberg Equilibrium. - Modified HWE.exact to return an object of class 'htest'. - Modified HWE.test to use HWE.exact by default for 2-allele genotypes, and HWE.chisq otherwise. genetics 0.6.7 -------------- - Added 'HWE.exact()', an exact test for Hardy-Wienberg Equilibrium for two alleles. Code contributed by David Duffy <davidD@qimr.edu.au> - Added 'gregorius()', which computes the probability of observing all alleles with a given frequency in a sample of a specified size.