News

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 [email protected]

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 [email protected].

• Added experimental, undocumented, and untested function hapmcmc for imputing haplotypes and related functions. (Code submitted by David Duffy [email protected]).

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 [email protected]

• Added 'gregorius()', which computes the probability of observing all alleles with a given frequency in a sample of a specified size.

Reference manual