August 25, 2010
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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49010 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 25/08/2010 02:32:48
August 21, 2010
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A few edits to copynumber vignette and sample.CNSetLM Rd file

Rob Scharp authored on 21/08/2010 02:50:25
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methods Ns, medians, corr, and mads return arrays.

Rob Scharp authored on 21/08/2010 02:50:19
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Added citation to crlmmCopynumber. Deleted many of the commented functions in cnrma-functions.R

Rob Scharp authored on 21/08/2010 02:50:15
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Changed totalCopyNumber to totalCopynumber to be consistent with caps in crlmmCopynumber. Fixed a few bugs in the .Rd files

Rob Scharp authored on 21/08/2010 02:50:10
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Edits to CA,CB, ACN accessors for copy number

Rob Scharp authored on 21/08/2010 02:50:05
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commented replacement method for snpCallProbability.

Rob Scharp authored on 21/08/2010 02:50:00
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Numerous changed to copy number estimation detailed below.

Rob Scharp authored on 21/08/2010 02:49:54
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A number of changes to fit.lm1 and crlmmCopynumber. The number of genotypes is now stored as part of the CNSet class object.

Rob Scharp authored on 21/08/2010 02:49:47
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Added methods for flags and flags<-. Added 'flags' as an element to the LinearModelParameter object

Rob Scharp authored on 21/08/2010 02:49:41
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Renamed computeCN crlmmCopynumber

Rob Scharp authored on 21/08/2010 02:49:37
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Removed args normal and snpflags from fit.lm* functions. Removed code that initializes the flag and snpflag matrices in computeCN

Rob Scharp authored on 21/08/2010 02:49:34
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Commented the 2 lines in fit.lm4 indicated below

Rob Scharp authored on 21/08/2010 02:49:31
Viewe63564b

begin commening the 'normal' matrix as this is not used.

Rob Scharp authored on 21/08/2010 02:49:25
View14bb412

Fixed cross-references that were not linked to a topic in CNSet-methods and copynumberAccessors Rd files

Rob Scharp authored on 21/08/2010 02:49:20