October 4, 2010
Viewfd0501a

Add illumina_copynumber.pdf to package.

Rob Scharp authored on 04/10/2010 02:21:53
August 30, 2010
Viewa070e5b

Replace match.fun with get.

Rob Scharp authored on 30/08/2010 19:41:22
View56b783e

Revised accesors in methods-AssayData -- some of the conflicts resolved by hand during rebase were incorrect

Rob Scharp authored on 30/08/2010 19:41:03
View0198a9a

Fixed several bugs in the CA, CB, ACN functions. Updated the copynumber vignette

Rob Scharp authored on 30/08/2010 19:40:42
View3e4db4b

constructIlluminaAssayData allows for either ff or matrices. Fixed bug in accessors for medians, mads, ...

Rob Scharp authored on 30/08/2010 19:40:33
August 21, 2010
View1715856

A few edits to copynumber vignette and sample.CNSetLM Rd file

Rob Scharp authored on 21/08/2010 02:50:25
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