August 30, 2010
Viewc6d091f

cleaned some of the temporary exports in the namespace

Rob Scharp authored on 30/08/2010 19:41:08
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
Viewd5b39e2

CB estimates were NA for SNP indices were mixed with NP indices. Bug was fixed in the ACN function

Rob Scharp authored on 30/08/2010 19:40:54
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
View52e58a4

Export plotCNSetLM for debugging.

Rob Scharp authored on 30/08/2010 19:40:28
View630adba

Exporting list and ffdf classes so that lM<- assignment works

Rob Scharp authored on 30/08/2010 19:40:16
August 25, 2010
View9a4a514

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
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
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