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Bioconductor Changlog.
Sat, 12 Jul 2008
VanillaICE
updated illuminahowto vignette
VanillaICE
do not evaluate code chunk 5 in illumina howto vignette
VanillaICE
changed one line in vignette
added copyNumber.scale option. needs to be a standard deviation on the appropriate scale
VanillaICE
check in sweave
VanillaICE
the viterbi algorithm was not handling NA emission probabilities appropriately. should be OK now
VanillaICE
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
VanillaICE
added accessors/replacement methods for HmmOptions class
VanillaICE
updated a few of the man pages
VanillaICE
Added Biobase to the Depends field.
VanillaICE
calls.ICE should be working now. updated vignettes
VanillaICE
mostly updates to add needed documentation
VanillaICE
changed class definitions of HmmOptions and HmmParameter. Initialization is (hopefully) more straightforward
VanillaICE
fixed bug in calculateBreakpoints. Removed ParHmm* classes
VanillaICE
allow option to plot vertical dashed lines for breakpoints. Updated the fit example data
VanillaICE
Added processed data object. Added inst/testing directory. Copy number should always be stored on the original scale
VanillaICE
updated how transition probabilities are passed to the viterbi. store emission probabilities in an array for HmmParameter
VanillaICE
changed the default for getting confidence scores to use a robust estimate for the across sd. See calculateCnSE
fixed broken links to ParESet
VanillaICE
changed the function calculateCnSE allows missing values for copy number. changed the show method for HmmPredict class
VanillaICE
pass beta argument in the initialize method for HmmParameter to the initialize method for HmmOptions
bug fix in the initialize methods. length(beta) is 1 if not specified
if emission probabilities is supplied to the initialize method for HmmParameter, several options in the HmmOptions class can be skipped...
VanillaICE
numerous changes to plotting methods (getPar). Added the featureData slot to the class defintion of HmmPredict, as well as a few more accessors
VanillaICE
Made a number of changes to the VanillaICE infrastructure. The main idea was to move away from storing SNP-level data and results from the HMM in the same R object. Classes HmmSnpSet, HmmSnpCopyNumberSet, and HmmSnpCallSet are defunct. Instead, we define a parameter class for the HMM -- HmmParameter -- and a class for storing the results from the HMM -- HmmPredict. The .Rd files were removed and rewritten. plotSnp methods were also modified to accomodate the changes in the class structure. In addition, a vignette was added to describe how one may create an instance of oligoSnpSet from BeadStudio processed data. The vignette VanillaICE.Rnw was rewritten. The example data, chromosome1, was changed to an oligoSnpSet.
VanillaICE
several updates to make the package compatible with SNPchip. Changed the annotation field in chromosome1 as well as the fvarLabels. Updated the vignette
VanillaICE
fixed bug in calculation of emission probability...
VanillaICE
changed licence in the description to LGPL