NEWS
genetics 1.3.8 (2012-12-15)
Bug fixes
- Regenerate broken PDF files in inst/doc.
genetics 1.3.7 (2012-08-14)
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 (2011-02-02)
- 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 (2008-04-30)
- 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 (2007-08-08)
- 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 (2006-12-12)
- Update Greg's email address
- Fixed a bug in function allele.number, as pointed out by Chris
Wallace
genetics 1.2.0 (2005-11-09)
- 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 (2004-12-23)
- 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 (2004-11-15)
- 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 (2004-09-21)
- 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 (2004-05-26)
- 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 (2003-06-04)
- 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 (2003-05-28)
- 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 (2003-04-07)
- 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.