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Sat, 10 May 2008
GeneticsBase
Change maintainer to R Genetics Project, with the mailing list email address
[/GeneticsBase] permanent link
Wed, 30 Apr 2008
GeneticsBase
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
[/GeneticsBase] permanent link
Thu, 24 Apr 2008
GeneticsBase
Correct description of power calculation example code
Remove unrelated material from HOWTO
The power.casectl function was performing and invalid calculation.
Replaced it with correct functions "GeneticsPower.Quantitative.Factor"
and "GeneticsPower.Quantitative.Numeric", and modified the
GeneticsBase Tutorial vignette to use the new functions. The old
function is only present as a stub, which raises a depreciated error
[/GeneticsBase] permanent link
Wed, 23 Apr 2008
GeneticsBase
Add numbers to code chunks in SummaryTables.Rnw to make errors easier to locate
[/GeneticsBase] permanent link
Sat, 15 Mar 2008
GeneticsBase
Update TODO from old changes
[/GeneticsBase] permanent link
Sat, 26 Jan 2008
GeneticsBase
Reneame the 'tutorial' vignette to 'Tutorial' to be consistent with capitalization of the other vignettes.
Update HWE.exact doc to include proper attribution and literature reference
Update TODO list based on telecon 2007-01-25
[/GeneticsBase] permanent link
Tue, 15 Jan 2008
GeneticsBase
Fix typos and minor reformatting
Add vignette 'tutorial' from BioC2007 tutorial session.
Add note that SummaryTables.Rnw vignette is designed for small number of markers
[/GeneticsBase] permanent link
Sat, 15 Dec 2007
GeneticsBase
Add as.geneSet.R source file to Collate
Add as.geneSet methods to NAMESPACE
Fix check and warning for alleles argument to makeCCodesAndTTables()
Fix typos
Fix typos
Add as.geneSet() function and documentation
Set pedigree-specific argument founderOnly to be FALSE by default, since it FAILS when pedigree information is not present. TODO: This should be changed to *detech* if pedigree information is present, then act appropriately. Also, correct he default value for confidence interval quantiles to be 2.5% and 97.5% rather than (usually incorrect) 95%.
Minor code reformatting
Fix handling when missing codes are specified by a single 'ALL' entry for all markers
Implement code for remove.spaces=TRUE, convert empty alleles to NA, correct behavior when only one column of genotypes is provided
[/GeneticsBase] permanent link