August 21, 2010
Viewfda1107

methods Ns, medians, corr, and mads return arrays.

Rob Scharp authored on 21/08/2010 02:50:19
View6b75ec7

Added citation to crlmmCopynumber. Deleted many of the commented functions in cnrma-functions.R

Rob Scharp authored on 21/08/2010 02:50:15
Viewdf2226f

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
View66900fe

Edits to CA,CB, ACN accessors for copy number

Rob Scharp authored on 21/08/2010 02:50:05
Viewada0da1

commented replacement method for snpCallProbability.

Rob Scharp authored on 21/08/2010 02:50:00
View6846d58

Numerous changed to copy number estimation detailed below.

Rob Scharp authored on 21/08/2010 02:49:54
Viewd08acba

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
View33a5ea6

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
Viewc45787d

Renamed computeCN crlmmCopynumber

Rob Scharp authored on 21/08/2010 02:49:37
View8800496

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
Viewe84db07

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
View69ec864

Added help files for copy number accessors. Fixed bugs in CA, CB, and total copy number methods.

Rob Scharp authored on 21/08/2010 02:49:14
View8160162

Updated sample.CNSetLM helpfile with coercion to v1.0.1 of the CNSet class definition

Rob Scharp authored on 21/08/2010 02:49:06