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2008-08-20 19:06 warnes
* DESCRIPTION, inst/NEWS: Bump version numer up and update NEWS
file
2008-08-20 19:04 warnes
* R/makeGenotypes.R: Fix bug in makeGenoypes that caused it to
ignore 'sep' when identifying potential genotype columns
2008-04-30 01:23 warnes
* man/depreciated.Rd: Add complete reference to GeneticsDesign
functions
2008-04-30 01:05 warnes
* DESCRIPTION, inst/NEWS: Update for version 1.3.3
2008-04-30 00:54 warnes
* R/genotype.R, R/locus.R: Replace obsolete (grr!) use of "$\" for
atomic vectors
2008-04-30 00:53 warnes
* R/power.casectl.R, man/depreciated.Rd, man/power.casectl.Rd: Mark
power.casectl() as depreciated in favor of GeneticsDesign
functions
2007-11-20 20:30 warnes
* R/expectedGenotypes.R: Add extra error checking to
expectedGenotypes()
2007-11-20 20:27 warnes
* DESCRIPTION, inst/NEWS: Update NEWS and DESCRIPTION for genetics
1.3.2
2007-11-20 20:25 warnes
* man/power.casectl.Rd: Fix documentation of kp and alpha arguments
to power.casectl()
2007-11-20 20:24 warnes
* R/hapmcmc.R: Add set argument to hapshuffle
2007-11-20 20:23 warnes
* R/power.casectl.plot.R: Add explicit variable definition to avoid
R CMD CHECK warning
2007-11-20 20:23 warnes
* R/zzz.R: Package startup message states package is OBSOLETE
2007-11-20 20:20 warnes
* R/genotype.R, tests/test.NA.R: Bug fix and regression test for
assignment of NA to element of existing genotype object
2007-09-12 10:41 ggorjan
* DESCRIPTION, NAMESPACE, R/genotype.R, R/summary.genotype.R,
inst/NEWS, man/genotype.Rd: - fixes in genotypeOrder to ensure
all genotype/haplotype combinations
are used.
- genotypeOrder<- is now exported
2007-08-21 14:37 warnes
* ChangeLog, NEWS: Add softlinks into inst/ for ChangeLog and NEWS
2007-08-21 14:36 warnes
* NEWS, inst/NEWS: Move Changelog (not in SVN) and NEWS to inst/
2007-08-21 14:35 warnes
* inst/ChangeLog, inst/NEWS: Remove softlinks in inst, doesn't work
on windows
2007-08-20 18:30 warnes
* inst/ChangeLog, inst/NEWS: Add softlinks in inst to NEWS and
ChangeLog so these will get installed.
2007-08-08 14:59 warnes
* DESCRIPTION: Bump minor version number since Gregor added new
functions
2007-08-08 14:58 warnes
* NEWS: Update NEWS file for new release
2007-08-08 14:56 warnes
* DESCRIPTION: Update description for release, add credit to other
contributors
2007-08-08 14:51 warnes
* R/zzz.R: Add note referring users to the R-Genetics project
homepage
2007-08-08 13:45 warnes
* NAMESPACE, R/binsearch.R, man/binsearch.Rd: Move binsearch() to
the gtools package
2007-08-08 13:38 warnes
* R/binsearch.R: Correct bug in binsearch. Elipses were omitted
from one cal to fun(). Bug reported by Matthew Walker
<m.g.walker@massey.ac.nz>
2007-07-25 07:32 ggorjan
* NAMESPACE, NEWS, R/expectedGenotypes.R, R/genotype.R,
R/groupGenotype.R, R/order.genotype.R, R/summary.genotype.R,
man/expectedGenotypes.Rd, man/genotype.Rd, man/groupGenotype.Rd,
man/order.genotype.Rd: groupGenotype(), some utility funcs, ...
2007-07-18 16:57 ggorjan
* NEWS, R/genotype.R: Fixed genotype() with
allow.partial.missing=FALSE when 'alleles'
argument is passed
Example:
## Old
> x <- c("C/C", "A/C", "A/A", NA, "C/B", "B/A", "B/B")
> alleles <- c("A", "B")
> genotype(x, alleles=alleles, allow.partial.missing=FALSE)
[1] NA "A/NA" "A/A" NA "B/NA" "B/A" "B/B"
Alleles: B A
Warning message: Found data values not matching specified
alleles. Converting to NA. in: genotype(x, alleles = alleles,
allow.partial.missing = FALSE)
## New
> genotype(x, alleles=alleles, allow.partial.missing=FALSE)
[1] NA NA "A/A" NA NA "B/A" "B/B"
Alleles: B A
Warning message: Found data values not matching specified
alleles. Converting to NA. in: genotype(x, alleles = alleles,
allow.partial.missing = FALSE)
> genotype(x, alleles=alleles, allow.partial.missing=TRUE)
[1] NA "A/NA" "A/A" NA "B/NA" "B/A" "B/B"
Alleles: B A
Warning message: Found data values not matching specified
alleles. Converting to NA. in: genotype(x, alleles = alleles,
allow.partial.missing = TRUE)
2007-07-18 16:32 ggorjan
* NEWS, R/genotype.R: 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
Here is the example:
## Old
> x <- c("C/C", "A/C", "A/A", NA, "C/B", "B/A", "B/B")
> alleles <- c("A", "B", "C")
> x <- genotype(x, alleles=alleles, reorder="yes")
Warning message:
Found data values not matching specified alleles. Converting to
NA. in: genotype(x, alleles = alleles, reorder = "yes")
> x
[1] "C/C" "A/C" "A/A" NA "B/C" "A/B" "B/B"
Alleles: A B C
## New
> x <- c("C/C", "A/C", "A/A", NA, "C/B", "B/A", "B/B")
> alleles <- c("A", "B", "C")
> x <- genotype(x, alleles=alleles, reorder="yes")
> x
[1] "C/C" "A/C" "A/A" NA "B/C" "A/B" "B/B"
Alleles: A B C
2007-07-18 14:22 ggorjan
* NEWS, R/diseq.R, man/diseq.Rd: really fixed printing of Obs vs
Exp freqs
2007-07-18 12:51 ggorjan
* R/expectedGenotypes.R, man/expectedGenotypes.Rd: sort produced
genotypes
2007-07-18 12:19 ggorjan
* R/expectedGenotypes.R: rollback one part
2007-07-18 12:09 ggorjan
* R/plot.genotype.R, man/plot.genotype.Rd: fixing S3 type of
documentation + minor fix
2007-07-18 12:08 ggorjan
* man/genotype.Rd, man/locus.Rd, man/print.LD.Rd,
man/summary.genotype.Rd: fixing S3 type of documentation
2007-07-18 11:57 ggorjan
* NEWS, man/power.casectl.Rd: Fixed documentation of
power.casectrl() to match its code
2007-07-18 11:49 ggorjan
* DESCRIPTION, NEWS, R/expectedGenotypes.R: added gtools to Depends
as needed by expectedGenotypes() + some minor fixes
2007-06-17 01:27 warnes
* man/power.casectl.Rd: Update with Michael's latest changes
2007-06-17 01:25 warnes
* R/power.casectl.plot.R: Move old code from power.casectl.R to
power.casectl.plot.R
2007-06-17 01:24 warnes
* R/power.casectl.R: Update with Michael's latest changes
2007-05-29 19:35 warnes
* NEWS: Add display of observed vs expected table to
print.HWE.test()
2007-05-29 19:34 warnes
* DESCRIPTION, man/HWE.test.Rd: Add display of observed vs expected
table to print.HWE.test()
2007-05-29 19:29 warnes
* R/HWE.test.R: Add display of observed vs expected table to
print.HWE.test()
2006-12-05 18:22 warnes
* man/undocumented.Rd: Remove typo/dupliucate alias entry for
ci.balance
2006-12-05 17:45 warnes
* NEWS: Update NEWS file for 1.2.0 and 1.2.1
2006-11-14 22:20 ggorjan
* trunk/GeneticsBase/DESCRIPTION, trunk/GeneticsBase/R/convert.R,
trunk/GeneticsBase/TODO.txt, trunk/GeneticsBase/data/ALZH.ped,
trunk/GeneticsBase/data/CAMP.ped,
trunk/GeneticsBase/data/CAMPZ.phe,
trunk/GeneticsBase/data/qtl.ped, trunk/GeneticsBase/data/qtl.phe,
trunk/GeneticsBase/data/xbat.ped,
trunk/GeneticsBase/data/xbat.phe,
trunk/GeneticsBase/man/fastGrid.Rd,
trunk/GeneticsBase/man/makeMarkerInfo.Rd,
trunk/GeneticsBase/man/makeTransTable.Rd,
trunk/GeneticsBase/man/makeTransTableList.Rd,
trunk/GeneticsBase/src/convert.c,
trunk/PopGenetics/R/HWE.test.data.frame.R,
trunk/PopGenetics/R/expectedGenotypes.R,
trunk/PopGenetics/R/plot.genotype.R,
trunk/PopGenetics/inst/doc/example_data.csv,
trunk/PopGenetics/man/expectedGenotypes.Rd,
trunk/PopGenetics/man/plot.genotype.Rd, trunk/fbat/DESCRIPTION,
trunk/fbat/data/CAMP.ped, R/HWE.test.data.frame.R,
R/expectedGenotypes.R, R/plot.genotype.R,
inst/doc/example_data.csv, man/expectedGenotypes.Rd,
man/plot.genotype.Rd: Removing executable property
2006-11-11 04:10 warnes
* DESCRIPTION: Update version number
2006-11-11 04:09 warnes
* DESCRIPTION, inst/doc/genetics_article.tex, man/HWE.exact.Rd,
man/HWE.test.Rd, man/LD.Rd, man/binsearch.Rd, man/ci.balance.Rd,
man/diseq.Rd, man/genotype.Rd, man/gregorius.Rd,
man/homozygote.Rd, man/locus.Rd, man/makeGenotypes.Rd,
man/print.LD.Rd, man/summary.genotype.Rd, man/write.pop.file.Rd:
Update my email address
2006-10-02 13:21 weiliang_qiu
* DESCRIPTION: add the 'BioCViews' tag with 'Genetics' as the
keyword to the
DESCRIPTION file
2006-03-10 18:19 nj7w
* R/write.pedigree.file.R: Fixed a bug in function allele.number,
as pointed out by Chris Wallace
2005-11-10 15:28 warnes
* man/HWE.exact.Rd, man/HWE.test.Rd, man/LD.Rd, man/binsearch.Rd,
man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd,
man/gregorius.Rd, man/homozygote.Rd, man/locus.Rd,
man/makeGenotypes.Rd, man/print.LD.Rd, man/summary.genotype.Rd,
man/write.pop.file.Rd: Update my email address
2005-11-09 17:05 warnes
* DESCRIPTION: Update version number and release date
2005-11-09 17:04 warnes
* R/HWE.test.R, R/LD.R, R/ci.balance.R, R/diseq.R, man/diseq.Rd:
Add R^2 to HWE and LD estimates
2005-11-08 20:54 warnes
* R/summary.genotype.R: Fix Heterozygosity correction, per
Christopher Carlson
<csc47@u.washington.edu>:
> My second question is with regard to the summary.genotype
> function. The value you return for Heterozygosity (Hu) appears
to be
> 2pq*(n/(n-1)), but with n as the number of individuals. I
believe
> that the proper correction is for n/(n-1) where n is the number
of
> chromosomes, not the number of individuals. For a reasonable
number
> of samples the difference is subtle, but it threw off my
Tajima's D
> estimates when I used Hu to calculate nucleotide diversity.
2005-10-04 23:43 warnes
* DESCRIPTION, NAMESPACE, R/diseq.R, R/expectedGenotypes.R,
R/power.casectl.R, R/print.LD.R, R/zzz.R: Move all dependency
checking into DESCRIPTION and NAMESPACES.
2005-10-04 16:30 warnes
* R/plot.genotype.R: Fix handling of the 'type' argument.
2005-10-04 16:28 warnes
* R/plot.genotype.R: Correct the handling of the 'what' argument.
2005-10-04 15:17 warnes
* DESCRIPTION: Forgot to increment version
2005-10-04 15:15 warnes
* DESCRIPTION: Update email address, version number, and date.
2005-10-04 15:13 warnes
* R/diseq.R: Return NA and issue a warning if diseq() called on a
marker with
only one observed allele.
2005-09-14 18:45 ggorjan
* R/plot.genotype.R: Now plot percentage by default i.e. no need
for argument in function call.
2005-08-18 19:39 nj7w
* R/genotype.R: Fix bug in heterozygote when more than one
allele.name is provided
2005-03-13 01:23 warnes
* R/library.R, man/library.Rd: Remove old backport of library()
commanad that is no longer needed.
2005-03-12 21:57 warnes
* R/summary.genotype.R: Change 'persons' to 'samples' so that we
aren't human-specific.
2005-03-12 21:54 warnes
* DESCRIPTION, NAMESPACE, man/expectedGenotypes.Rd,
man/plot.genotype.Rd: Fixes to pass R CMD check after addition of
expectedGenotypes() and
plot.genotype().
2005-03-12 20:23 warnes
* R/plot.genotype.R, man/plot.genotype.Rd: Add plot.genotype()
contributed by Gregor GORJANC
2005-03-12 20:22 warnes
* R/expectedGenotypes.R, man/expectedGenotypes.Rd: Add
expectedGenotypes() contributed by Gregor GORJANC
2005-03-09 19:49 warnes
* man/makeGenotypes.Rd: Add description of the use of the 'method'
argument, and an example
showing the use of 'method=as.genotype.allele.count'.
2005-03-02 18:14 nj7w
* NAMESPACE: Fixed NAMESPACE file to import na.omit function
explicitly from stats package.
2004-12-23 01:34 warnes
* R/HWE.test.data.frame.R, inst/doc/LD.pdf,
inst/doc/example_data.csv, inst/doc/genetics_article.pdf: Check
in some files that seem to have been overlooked in the past.
2004-12-23 01:21 warnes
* NEWS: Update for 1.1.2 (and 1.1.1).
2004-12-23 01:14 warnes
* DESCRIPTION: Update version number.
2004-12-23 01:08 warnes
* R/diseq.R: Remove debugging code that printed intermediate values
(sometimes a
lot of them).
2004-11-22 14:35 warnes
* man/LD.Rd: Fix typos.
2004-11-15 16:36 warnes
* DESCRIPTION: Update version.
2004-11-15 16:22 warnes
* R/summary.genotype.R: Ensure that allele.freq table has the same
ordering as allele.names.
2004-11-15 16:20 warnes
* R/HWE.test.R: remove triplicate comment
2004-11-15 15:34 warnes
* man/HWE.chisq.Rd: 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.
2004-10-13 16:21 warnes
* R/diseq.R, man/diseq.Rd: Attempt to fix/clarify HWE diseq.
computations & synchronize documentation.
2004-09-21 21:45 warnes
* DESCRIPTION, NAMESPACE, NEWS, R/power.casectl.R,
man/HWE.chisq.Rd, man/HWE.exact.Rd, man/HWE.test.Rd,
man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd,
man/homozygote.Rd, man/locus.Rd, man/power.casectl.Rd,
man/summary.genotype.Rd, man/undocumented.Rd: Updated to use a
namespace and to work with the lastest gregmisc
bundle (previously a package).
2004-09-17 18:46 warnes
* man/HWE.chisq.Rd, man/HWE.exact.Rd, man/HWE.test.Rd, man/LD.Rd,
man/binsearch.Rd, man/ci.balance.Rd, man/diseq.Rd,
man/genotype.Rd, man/gregorius.Rd, man/homozygote.Rd,
man/library.Rd, man/locus.Rd, man/makeGenotypes.Rd,
man/power.casectl.Rd, man/print.LD.Rd, man/summary.genotype.Rd,
man/undocumented.Rd, man/write.pop.file.Rd: Comments were
incorrectly marked by '#' instead of '%'.
2004-09-16 22:15 warnes
* R/power.casectl.R: Changes from Michael Man.
2004-09-16 21:33 warnes
* man/diseq.Rd: Match changes to print.diseq revision 1.16, which
restored ability
to show Observed vs. Expected table by addition an additional
potential value for the 'show' parameter: "table".
2004-09-16 21:22 warnes
* NAMESPACE: Add namespace.
2004-09-15 18:32 warnesgr
* R/diseq.R: Restore ability to show Observed vs. Expected table by
addition an
additional potential value for the 'show' parameter: "table".
2004-07-02 15:57 warnesgr
* R/power.casectl.R, man/power.casectl.Rd: Add power.casectl
provided by Micheal Man.
2004-05-25 19:40 warnesgr
* DESCRIPTION, R/genotype.R, R/print.LD.R, man/HWE.test.Rd,
man/binsearch.Rd, man/genotype.Rd, man/locus.Rd,
man/makeGenotypes.Rd, man/undocumented.Rd: Many fixex.
2004-03-25 17:15 warnesgr
* R/ci.balance.R, man/ci.balance.Rd: Remove unused '...' argument
from ci.balance.
2004-02-02 15:55 warnesgr
* R/ci.balance.R, R/diseq.R, man/ci.balance.Rd: - Rename ci.balance
'conf' parameter to 'confidence', and add 'alpha'
parameter to remove R CMD check warning.
- modify diseq.ci to pass confidence level to ci.balance.
2004-02-02 15:46 warnesgr
* man/homozygote.Rd: remove extraneous period from argument to
carrier.genotype.
2003-12-02 18:41 warnesgr
* R/genotype.R: - remove depreciated (and error prone) use of
codes().
2003-12-02 18:37 warnesgr
* R/print.LD.R: - Fixed bug: "D" was being reported when only "D'"
was requested.
2003-11-24 17:32 warnesgr
* man/write.pop.file.Rd: - Fix the last broken fix.
2003-11-24 17:22 warnesgr
* man/write.pop.file.Rd: Changes to fix latex'ing problem.
2003-08-04 14:18 warnesgr
* DESCRIPTION, NEWS: - Updated NEWS and DESCRIPTION for version
1.0.2
2003-08-04 13:48 warnesgr
* R/summary.genotype.R: - Fixed a bug in Heterozygosity (H) and PIC
calcuations caused by
using allele count rather than allele proportions. Bug reported
by
Gerard Tromp <tromp@sanger.med.wayne.edu>.
2003-07-30 20:39 warnesgr
* R/hapmcmc.R: - Added hapmcmc code submitted by David Duffy.
2003-06-06 09:27 warnesgr
* man/binsearch.Rd, man/library.Rd, man/print.LD.Rd: - Fix
fuction/documententation argument mismatch.
- Fix lack of LF at the end of a couple of files.
2003-06-05 22:06 warnesgr
* R/summary.genotype.R: - Added code to show number of alleles,
number of individuals
genotyped, heterogyosity, and poly. information content based on
code contribued by David Duffy.
2003-06-04 21:22 warnesgr
* R/plot.LD.R: - Modified string size to only leave vertical space
for the number of
elements that will be printed.
2003-06-04 21:22 warnesgr
* R/genotype.R: - Somehow the assigment of the haplotype function
got messed up. Fixed.
2003-06-04 21:21 warnesgr
* man/print.LD.Rd: - Updated manual to match code
- Replaced 'T' with 'TRUE'
2003-06-04 21:20 warnesgr
* R/print.LD.R: - summary functions should have 'object' as the
first parameter.
2003-06-04 20:26 warnesgr
* DESCRIPTION, NEWS, TODO: Updates for release 1.0.1.
2003-06-04 20:20 warnesgr
* R/plot.LD.R, R/print.LD.R, man/print.LD.Rd: - Fixed mislabeling
of rows/columns in LDtable
- Extended LDtable to handle resizing text to fit area
- Extended LDtable to allow slection of what 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 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
2003-06-03 12:59 warnesgr
* R/LD.R: - LD.genotype needs to reject haplotype objects since
these are not
yet supported by the code.
2003-06-03 11:41 warnesgr
* R/genotype.R: - Fix handling of allele names when reorder="no".
Apparently,
unique() on a matrix now returns a matrix with unique *rows*
removed,
instead of a vector of unique *elements*. The consequence in this
case was that genotype(...,reorder="no") was generating a list of
alleles that was a matrix instead of a vector.
2003-05-30 16:08 warnesgr
* man/locus.Rd: - added documentation for "value" option.
2003-05-30 15:52 warnesgr
* R/library.R, R/zzz.R: - library.pos will now always be defined.
Instead of conditionally
defining library.pos, a check is made in .First.lib to see
whether
the system library function has a pos argument. If not, it uses
library.pos instead of library to load dependencies.
2003-05-29 02:27 warnesgr
* inst/doc/genetics_article.tex: - added ld to conclusion text
2003-05-29 02:23 warnesgr
* inst/doc/genetics_article.tex: Updated for version 1.0.0
2003-05-29 02:22 warnesgr
* DESCRIPTION, NEWS: - Updated for 0.7.0
2003-05-29 02:20 warnesgr
* inst/doc/genetics_article.tex: - Final version to send to Fritz.
2003-05-29 01:55 warnesgr
* inst/doc/example.R, inst/doc/genetics_article.tex,
inst/doc/make_example_data.R: - Add R code to generate and demo
genetics package
2003-05-29 00:36 warnesgr
* R/locus.R: - All arguments are now optional.
2003-05-29 00:35 warnesgr
* R/genotype.R: - Fix problem with NA's caused by grep bug in R <=
1.7.0.
2003-05-28 20:28 warnesgr
* man/locus.Rd: - Add getmarker, getgene, locus<- , marker<-, and
gene<- functions.
2003-05-28 20:26 warnesgr
* man/write.pop.file.Rd: - Add URL for LinkDos
2003-05-28 20:26 warnesgr
* man/undocumented.Rd: - Add alias for to shortsummary function.
2003-05-28 15:09 warnesgr
* man/LD.Rd: - Added "locus<-", "marker<-", "gene<-", as well as
"getgene", "getmarker"
2003-05-28 15:04 warnesgr
* man/library.Rd: - renamed library() to library.pos(). Updated
text to correcty note
that the backport is from 1.8.0.
2003-05-28 15:01 warnesgr
* R/write.pedigree.file.R: - Renamed write.pedigree to
write.pedigree.file.
- Added URL of LinkDos software.
2003-05-28 14:57 warnesgr
* R/library.R, R/zzz.R: - Rename library to library.pos
2003-05-28 14:56 warnesgr
* R/locus.R: - Added "locus<-", "marker<-", "gene<-", as well as
"getgene", "getmarker"
2003-05-27 21:18 warnesgr
* R/print.LD.R, man/print.LD.Rd: - Added show.all argument
- Fixed code that omits blank row/column
2003-05-27 19:37 warnesgr
* man/write.pop.file.Rd: - Add documentation for write.pop.file,
write.pedigree.file, write.marker.file.
2003-05-27 18:45 warnesgr
* man/diseq.Rd, man/genotype.Rd, man/makeGenotypes.Rd,
man/summary.genotype.Rd: - Fix typos, update arguments to match
changes to code
2003-05-27 18:43 warnesgr
* R/library.R, man/library.Rd: - Added temporary copy of library()
function. This copy will only be
installed if the global library() function does not define a
'pos'
argument. This code was backported from R-devel, and R 1.7.1 and
later will include it as part of base.
2003-05-27 18:41 warnesgr
* R/write.pedigree.file.R, R/write.pop.file.R: - Add utility
functions to write pedigree, 'pop', and marker files
which are used to transfer data to genetics applications.
2003-05-27 18:36 warnesgr
* R/zzz.R: - Use new library function to load MASS in search
position *3* before
loading gregmisc. This prevents the genotype dataset in MASS from
hiding the genotype function here.
2003-05-27 18:35 warnesgr
* R/genotype.R: - fixed handling of genotype("") and similar
- improvements to "[<-.genotype", it now automatically converts
the
second argument to a genotype object.
2003-05-27 18:33 warnesgr
* R/diseq.R: - Add call item to diseq.object giving original
function call
- Fixed bug in testing for 2 x 2 allele case
2003-05-27 18:32 warnesgr
* R/plot.LD.R, R/print.LD.R, man/print.LD.Rd: - Add plot and print
methods for LD objects.
2003-05-27 18:30 warnesgr
* R/LD.R: - Found and fixed bug in likelihood computation. The
count table
needed to be organized with high-frequency alleles in the upper
left
corner instead of the lower right corner.
2003-05-22 17:25 warnesgr
* R/HWE.chisq.R, R/HWE.exact.R, R/HWE.test.R, R/LD.R,
R/binsearch.R, R/ci.balance.R, R/genotype.R, R/gregorius.R,
R/locus.R, R/makeGenotypes.R, R/plot.LD.R, R/print.LD.R,
R/summary.genotype.R, R/zzz.R: - Remove CVS Log tag, which was
eating up too much space. Just use
'cvs log' to get the comments if needed!
2003-05-22 16:22 warnesgr
* R/LD.R, R/plot.LD.R, R/print.LD.R: - moved LD printing functions
to print.LD.R
- moved LD plotting functions to plot.LD.R
- fixed problems in print.LD.data.frame
- enhanced plot.LD.data.frame
- other small changes
2003-05-21 20:03 warnesgr
* R/makeGenotypes.R: - Remove stray character that caused a syntax
error.
2003-05-21 20:03 warnesgr
* R/summary.genotype.R: - Fix handling of genotype summary when
called from
summary.data.frame. Was broken by too-broad search and
replace... but the changes motivated enhancements. ;^)
2003-05-21 19:57 warnesgr
* DESCRIPTION, R/zzz.R: - Added dependency on gregmisc package.
2003-05-21 19:46 warnesgr
* R/LD.R, man/LD.Rd, man/print.LD.Rd: - Improvements to LD code and
documentation.
2003-05-20 16:46 warnesgr
* R/makeGenotypes.R, man/makeGenotypes.Rd: - Reduce stringency for
considering a variable a genotype.
2003-05-20 16:43 warnesgr
* R/LD.R, man/LD.Rd: - Add code & (incomplete) docs for linkage
disequilibrium
2003-05-16 18:39 warnesgr
* DESCRIPTION, R/makeGenotypes.R, inst/doc/Rnews.sty,
inst/doc/genetics_article.tex, man/makeGenotypes.Rd: - Updated to
version 0.7.0
- Made changes to pass R CMD check
2003-05-16 15:50 warnesgr
* R/makeGenotypes.R, man/makeGenotypes.Rd: - Added
makeGenotypes/makeHaplotypes to help convert variables in
dataframes to genotype/haplotype variables.
2003-04-07 20:30 warnesgr
* R/diseq.R, man/diseq.Rd: - Flipped sign of D, D', r. Now D
matches sign given in Weir's book,
and r has the proper sign.
2003-03-07 14:52 warnesgr
* R/HWE.exact.R, man/HWE.exact.Rd: - Modified HWE.exact to return
an object of class 'htest'
- Noted this change in the man file and added HWE.chisq to list
of
links and to example code.
2003-03-07 14:49 warnesgr
* DESCRIPTION: - Updated version number to 0.6.7.
2003-03-07 14:47 warnesgr
* man/HWE.test.Rd: - Added links to HWE.chisq, HWE.exact, genotype
to see also seciton.
- Slighlty modified example code.
2003-03-07 14:44 warnesgr
* NEWS: - New file
2003-03-07 14:33 warnesgr
* R/genotype.R, man/genotype.Rd: - Added nallele function to
compute the number of alleles.
2003-03-07 14:32 warnesgr
* R/HWE.chisq.R, R/HWE.test.R, man/HWE.chisq.Rd, man/HWE.test.Rd: -
Created HWE.chisq, HWE.chisq.genotype and corresponding man page.
- Moved computation of Chisquare test for HWE from
HWE.test.genotype
to HWE.chisq.genotype.
- Added option (on by default) to compute the exact p-value using
HWE.exact.
This is on by default when nallele=2
2003-02-03 16:13 warnesgr
* DESCRIPTION, inst/doc/genetics_article.tex, man/HWE.exact.Rd,
man/binsearch.Rd, man/gregorius.Rd: - Fixed typos and R CMD check
warnings.
- Updated version number
- Removed 'data' directory to fix new R CMD check warning.
2002-12-11 21:29 warnesgr
* R/binsearch.R: - fixed typo
2002-12-11 21:07 warnesgr
* R/binsearch.R, R/gregorius.R, man/binsearch.Rd, man/gregorius.Rd:
- Moved binsearch() into a separate file and added documentation.
- Simplified and documented binsearch() code.
- binsearch() now detects whether the function is increasing or
decreasing and acts accordingly.
- Updated gregorius() to use the modified binsearch.
2002-12-10 20:36 warnesgr
* man/gregorius.Rd: - Updated title/description
2002-12-10 20:33 warnesgr
* R/gregorius.R, man/gregorius.Rd: - Implemented gregorius()
function, replacing data frame gregorius.
- Re-created corresponding help page.
2002-12-02 17:23 warnesgr
* man/gregorius.Rd: - Added cvs tags to header of gregorius.Rd
2002-12-02 17:13 warnesgr
* data, data/00Index, data/gregorius.R, man/gregorius.Rd: - Added
data set (and documentation) 'gregorius' which contains
necessary samples sizes to detect alleles.
2002-12-02 16:16 warnesgr
* man/HWE.exact.Rd: - Added HWE.exact.Rd.
2002-12-02 16:12 warnesgr
* R/HWE.exact.R: - Now returnes only the computed P-value.
2002-12-02 15:40 warnesgr
* R/HWE.exact.R: - Added code for HWE.exact, based on contributed
function by David
Duffy <davidD@qimr.edu.au>
2002-11-27 15:32 warnesgr
* DESCRIPTION, R/HWE.test.R, R/diseq.R, R/genotype.R, TODO,
inst/doc/genetics_article.tex, man/HWE.test.Rd,
man/ci.balance.Rd, man/diseq.Rd, man/genotype.Rd, man/locus.Rd,
man/summary.genotype.Rd, man/undocumented.Rd: Correct spelling
errors and typos.
2002-11-13 20:18 warnesgr
* DESCRIPTION: - Fix typo.
2002-11-12 19:59 warnesgr
* DESCRIPTION, R/diseq.R, R/genotype.R: - Changes to remove
warnings generated by 'R CMD check'.
2002-11-12 19:58 warnesgr
* man/HWE.test.Rd, man/ci.balance.Rd, man/diseq.Rd,
man/genotype.Rd, man/homozygote.Rd, man/locus.Rd,
man/summary.genotype.Rd, man/undocumented.Rd: - Changes to remove
warnings generated by 'R CMD check'.
2002-11-12 17:57 warnesgr
* R/zzz.R: - diseq.ci now requires the combinat library instead of
boot.
2002-11-12 05:53 warnesgr
* examples/test.ci.R: - Checkin of test.ci.R
2002-11-12 05:31 warnesgr
* DESCRIPTION: - Bump version number
2002-11-12 05:31 warnesgr
* R/genotype.R, R/locus.R, man/diseq.Rd, man/genotype.Rd,
man/homozygote.Rd: - Fix mismatches between documentation and
code that we generating
warning messages.
2002-11-11 22:56 warnesgr
* R/diseq.R: - Added minval and maxval to ci.balnance call() in
diseq.ci()
- Fixed typo in output text.
2002-11-08 21:07 warnesgr
* DESCRIPTION, R/genotype.R, R/summary.genotype.R, TODO,
man/HWE.test.Rd, man/genotype.Rd, man/homozygote.Rd,
man/locus.Rd, man/summary.genotype.Rd, man/undocumented.Rd: -
DESCRIPTION: Updated version number and date
- TODO: Updated todo list.
2002-11-08 19:54 warnesgr
* tests, tests/ci.balance.R: Added tests for ci.balance() functon.
2002-11-08 19:53 warnesgr
* R/ci.balance.R, R/diseq.R, man/ci.balance.Rd, man/diseq.Rd: -
Moved ci.balance() to a separate file and created a documenation
file for it.
- Modified ci.balance to better annotate when it uses boundary
values.
- Modified diseq.ci to better provide warning message when the
number of
alleles is greater than 3.
2002-11-08 17:20 warnesgr
* R/HWE.test.R, R/diseq.R: - Added test for more than two alleles
to diseq.ci. If there are more
than two, generate a warning message indicating that confidence
intervals for values near 0 and 1 are ill-behaved. When
'correct=TRUE' use ci.balance to attempt to correct for this.
- Modified HWE.test to display warnings from diseq.ci.
2002-11-07 19:13 warnesgr
* R/diseq.R: - Fixed code so that gentypes with some listed allele
not observed are
handled properly. For example, if we have "A/A", and "A/B", but
no
"B/B", or worse yet when we know that "A" and "B" allels are both
possible but we only see one.
2002-10-28 18:20 warnesgr
* R/genotype.R: - Allow allele names to be specified for
as.genotype.allele.count().
2002-10-28 18:19 warnesgr
* R/summary.genotype.R: - Fixed for syntax error in
summary.genotype()
2002-10-28 18:19 warnesgr
* R/HWE.test.R, R/diseq.R: - Lots of changes to the disequlibrim
computation and confidence interval code.
- D, D', and R are now computed
- Overall values are reported *with sign* of the number of
alleles is 2
- Bootstrapping code is now more efficient
- Changes to HWE.test() and print.hwe.test() corresponding to the
above changes
2002-10-24 21:43 warnesgr
* DESCRIPTION, R/diseq.R, R/genotype.R, man/genotype.Rd: - Fixed
bug as.genotype.alllele.count() introduced when 'harmonizing'
methods
with generics.
- Added 'alleles' arguments to the as.genotype.alllele.count()
function.
- Added example code for as.genotype.alllele.count() to doc file.
- Added explicit mention of as.genotype.alllele.count() to doc
file.
2002-10-11 18:01 warnesgr
* R/HWE.test.R, R/diseq.R, R/zzz.R: Updated version number.
2002-09-30 14:35 warnesgr
* R/diseq.R: - Modified diseq() to retain sign on the overall
disequlibrium estimate
- Modified diseq.ci() to use percentile confidence intervals
2002-09-24 01:53 warnesgr
* DESCRIPTION: - Updated version number
- Added 'computing disequilibrium' to description text.
2002-09-24 01:32 warnesgr
* R/HWE.test.R, R/diseq.R, R/genotype.R, R/zzz.R, man/HWE.test.Rd,
man/diseq.Rd, man/genotype.Rd, man/summary.genotype.Rd: -
'Un-genericized' diseq()
- Moved documentation of diseq() and diseq from HWE.test.Rd to
diseq.Rd
- Cleaned up HWE.test.Rd and diseq.Rd
- Fixed broken class check in diseq() and diseq.ci()
- Removed allele.count.default() -- this will force the user to
explicitly call 'genotype' on the data to use allele.count().
- Added zzz.R to require package 'boot'
2002-09-24 00:02 WarnesGR
* R/HWE.test.R, R/diseq.R, man/HWE.test.Rd: - Moved code that
computed D-hat to diseq() and diseq.genotype() in diseq.R.
- Added diseq.ci() to compute confidence interval for D-hat.
- Added code to call diseq() and diseq.ci() from HWE.test()
- Added arguments to HWE.test() and print.HWE.test() to control
these new features
- Added text to HWE.test.Rd documenting these new functions and
arguments
2002-09-23 20:08 warnesgr
* R/genotype.R: - Added as.genotype.table()
2002-06-27 18:46 warnesgr
* inst/doc/genetics_article.tex: - More revisions. Hopefully last
set before submission to publication
review.
2002-06-27 18:46 warnesgr
* R/HWE.test.R, examples/HWE_Test.R: - Allow user to specify
parameters for the chisquare test.
2002-06-25 21:38 warnesgr
* inst/doc/genetics_article.tex: - Fixed syntax errors
- Some reorganization
2002-06-19 11:17 warnesgr
* man/locus.Rd: - Fixed typo in \seealso.
2002-06-19 10:34 warnesgr
* inst/doc/genetics_article.tex: Much enhancement, including
addition of example section.
2002-06-19 00:13 warnesgr
* R/HWE.test.R: - Fixed bug that caused 'Error: subscript out of
bounds' when a 2
allele genotype had 1/1 and 1/2 but not 2/2.
2002-06-18 20:42 warnesgr
* DESCRIPTION: Updated version.
2002-06-18 20:41 warnesgr
* R/genotype.R, man/summary.genotype.Rd: - Fixed a bug in
allele.count that resulted in infinite recuresion.
- Modified documentation to match changed code.
2002-06-18 19:38 warnesgr
* DESCRIPTION, R/genotype.R, R/summary.genotype.R, man/HWE.test.Rd,
man/genotype.Rd, man/locus.Rd, man/summary.genotype.Rd: Changes
to fix problems reported by R CMD check.
2002-05-06 18:35 swietm
* 7, TODO: Testing CVS functionality. Removed addewd characters to
TODO
2002-05-06 18:31 swietm
* 7, TODO: This was a test to learn how to add and modify files
using CVS
2002-04-09 00:49 warneg
* inst, inst/doc, inst/doc/Rnews.sty,
inst/doc/genetics_article.tex: - Initial checkin of article
sources
2002-04-08 23:24 warneg
* DESCRIPTION, man/homozygote.Rd: First checkin after moving
repository from tuwein.
2002-04-08 23:23 warneg
* man/genotype.Rd: - Noted that when the user specifies the alleles
non-matching elements
are converted to NAs.
2002-04-08 23:19 warneg
* R/genotype.R: - Modified 'genotype' function so that when the
user specifies the
alleles non-matching elements are converted to NAs.
2002-02-21 03:09 warnes
* R/genotype.R, man/genotype.Rd, man/undocumented.Rd: - Add
as.factor.genotype.
2002-02-14 12:55 warnes
* DESCRIPTION: Rephrased description.
2002-02-14 12:55 warnes
* R/HWE.test.R, R/genotype.R: Fixed bugs in [.genotype and
[.haplotype.
- There was a serious typo that would have been cought had I just
done
R CMD check.
- Revamped [.genotype and [.haplotype to work correctly and to
avoid
the overhead of calling genotype() or haplotype() when drop=T. I
think these finally work properly.
2002-02-14 12:48 warnes
* man/HWE.test.Rd, man/genotype.Rd, man/undocumented.Rd: - Added
'keywords' to HWE.test
- Create undocumented.Rd to satisfy documentation requiremets for
objects not otherwise included in documentation
- Add 'alais' commands noting that 'genotype' and '[.haplotype'
are
documented here.
2002-02-14 12:37 warnes
* man/genotype.Rd: - Small change to the example code.
2002-02-09 00:47 warnes
* R/genotype.R: - Fixed the changes to "[.genotype" and
"[.haplotype". I was
incorrectly coping *all* of the attributes in the case of drop=T.
This caused mis-labeling of the underlying factor levels.
2002-02-07 17:08 warnes
* man/genotype.Rd: Added examples related to two bugs,
- == with non-genotype/non-haplotype rhs, and
- [...,drop=T] .
2002-02-07 16:57 warnes
* R/genotype.R: Fixed two bugs
1) "[.genotype" and "[.haplotype" didn't have the 'drop'
argument, so
an error would be generated when used in a context that expected
it (like
lm(..., subset=something) ).
I've implemented these so that drop=T not only drops unused
factor
levels, but also drops unused *allele* levels.
2) "==.genotype" and "==.haplotype" didn't handle second
arguments that
weren't genotypes / haplotypes, so
x <- genotype( "A/B" )
x == "A/B"
would generate an error. Solved by converting the y argument to a
genotype / haplotype before the comparison.
Note that if the lhs is a genotype this means
x == "A/B"
and
x == "B/A"
give the identical results.
2001-08-13 15:36 warnes
* R/HWE.test.R: BUGFIX: Corrected problem where the allele order
was not consistent between
the first (Observed #) and second columns (Expected #) of the
HWE.test table. This caused incorrect values for Obs-Exp to
be calcuated, as well as incorrect D-hat estimates.
Fortunately, it did not effect the correctness of the test
statistic or p-value, since these were computed via the chisq
function.
2001-08-03 11:33 warnes
* DESCRIPTION, man/genotype.Rd: Minor changes.
2001-06-28 19:26 warnes
* R/chisq.test.R: Will let Fritz and Kurt negotiate any
changes/modifications to chisq.test.
2001-06-28 19:23 warnes
* R/genotype.R: Minor change, mask off extra attributes when
calling print() to
dislplay genotype data.
2001-06-28 19:15 warnes
* man/HWE.test.Rd: - Updated to match v1.4 of HWE.test.R.
- Added CVS id and log fields to file.
2001-06-28 19:14 warnes
* R/HWE.test.R: - Modified to use
chisq.test(...,simulate.p.value=T,B=10000) to use
simulated p-value so that assumptions underlying Chi-square
approximation need not hold. This particularly useful for small
sample sizes or when some allele pairs are not observed.
- Now gives a table of observed counts, observed frequency,
expected
frequency, and disequilibrium statistic (D-hat) for each pair of
alleles in addition to the overall disequilibrium statistic
(D-hat).
2001-06-15 17:02 warnes
* DESCRIPTION, R/HWE.test.R, R/chisq.test.R, R/genotype.R, TODO,
examples/Genomics.examples, man/HWE.test.Rd, man/genotype.Rd,
man/homozygote.Rd, man/locus.Rd, man/summary.genotype.Rd: -
Modified HWE.test to use chisq.test. Added a modified version of
chisq.test until the (minor) changes show up in ctest.
- Fixed documentation links and alias omissions
- Fixed getallele() to snag allele element or attribute if either
is
present. This makes it work for summary.genotype as well as for
genotype.
2001-06-13 20:00 warnes
* R/summary.genotype.R: - Added "allele.names" attribute.
2001-06-13 17:03 warnes
* R/HWE.test.R, man/genotype.Rd: - Updated HWE.test.R to not assume
that a summary.genotype object
contains the original genotype object.
- Removed a duplicate link to "allele.names" from genotype.Rd.
2001-05-30 22:15 warnes
* man/HWE.test.Rd: Added HWE.test.Rd to document HWE.test.
2001-05-30 22:12 warnes
* R/HWE.test.R, R/genotype.R, R/locus.R, TODO,
examples/Genomics.examples, man/genotype.Rd, man/homozygote.Rd,
man/summary.genotype.Rd: Updated documentation mostly. Added
as.character.genotype().
2001-05-30 22:03 warnes
* man/locus.Rd: Initial version of locus.Rd.
2001-05-29 17:42 warnes
* man/summary.genotype.Rd: Updated to note that row for NA is only
present if the data contains
NA. Corresponds to revision 1.2 of summary.genotype.R.
2001-05-29 17:38 warnes
* man/genotype.Rd, man/summary.genotype.Rd: Modified seealso().
2001-05-29 17:16 warnes
* man/homozygote.Rd: Completed homozygote.Rd which documents
homozygote(), heterozugote(),
carrier(), allele(), and allele.cound().
2001-05-29 10:27 leisch
* R/summary.genotype.R: add NA line only if NA's are present
2001-05-26 00:28 warnes
* man/homozygote.Rd: Partially completed man/homozygote.Rd
containing documentation for
homozygote(), heterozygote(), carrier(), allele.count(), and
allele().
2001-05-26 00:26 warnes
* R/genotype.R: Removed allele.ind() and added "any" parameter to
carrier(). When
more than one allele is selected, or when no alleles are slected
and
any=F, carrier() now acts as allele.ind() did.
Modified allele.count() to have similar behavior.
2001-05-25 23:39 warnes
* man/genotype.Rd: Added man/genotype.Rd to document genotype and
haplotype classes in
R/genotype.R.
2001-05-25 23:37 warnes
* R/genotype.R, R/summary.genotype.R, man, man/summary.genotype.Rd:
Moved summary.genotype and print.summary.genotype into a separate
file
(R/summary.genotype.R). Added man/summary.genotype.Rd containing
documentation for summary.genotype.
2001-05-22 20:26 warnes
* R/Gene.R, R/Genomics.R: classes defined in Gene.R substantially
rewritten and moved to locus.R.
Contents of Genomics.R moved to genotype.R.
2001-05-22 20:23 warnes
* examples/locus.example.R: Added more examples
2001-05-22 19:00 warnes
* examples/locus.example.R: Initial checkin of test script for code
in locus.R.
2001-05-22 18:58 warnes
* R/locus.R: - Renamed "location.X" to "as.character.X" to better
represent thier
function. (Note as.character isn't generic at the moment, so
these
functions must be called directly.)
- added function getlocus() to grab the appropriate locus field
or
attribute from an arbitrary object.
2001-05-22 18:53 warnes
* R/genotype.R: - Renamed "genotype.R" from "Genomics.R".
- Added slot for "locus" into genotype class.
- Made allele.count, allele.ind, heterozygote, homozygote, and
carrier
return objects with the same class and created print.X routines.
This enabled the next item..
- Made "locus" propagate to summary, HWE.test, allele,
allele.count,
allele.ind, heterozygote, homozygote, and carrier. This should
make
it easier to keep track of what locus each of these correspond
to.
**This may create unanticipated side effects**
2001-05-22 18:21 warnes
* R/locus.R: Created classes for "locus", "gene", and "marker"
along with basic
methods is.X, print.X, and generic utility function "location",
which
formats the locus infromation for printing.
2001-05-16 12:58 leisch
* R/Genomics.R: cosmetics
2001-05-16 12:55 leisch
* R/Genomics.R: genotype: bugfix for non-character allele vectors
(e.g., integers)
a2 is now ignored if a1 is a genotype
a1 can now also be a 2 column matrix of alleles
2001-05-10 16:15 leisch
* DESCRIPTION: update
2001-05-10 16:07 leisch
* R/Genomics.R: cosmetics
2001-05-07 13:22 warnes
* examples, examples/Allele_Freq.R, examples/Allele_Freq.out,
examples/Examples.new, examples/Examples.out,
examples/Gene.examples, examples/Genomics.examples,
examples/HWE_Test.R, examples/HWE_Test.out,
examples/test.data.2.txt, examples/test.data.txt: Added example
files, code, and output.
2001-05-07 13:21 warnes
* R, R/Gene.R, R/Genomics.R: Imported R code for
- Genotype and Haplotype classes,
- corresponding summary function (gives allele and genotype
frequencies)
- Hardy-Weinburg Equilibrium testing.
Also, a initial try at a Gene and Marker classes.
2001-05-03 13:07 leisch
* ., DESCRIPTION: Initial revision
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