@@ -1,22 +1,22 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.9.9

+Version: 1.9.10

 Date: 2010-12-10

-Author: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry

-Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

+Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry

+Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms

 License: Artistic-2.0

-Depends: R (>= 2.11.0),

+Depends: R (>= 2.13.0),

          methods,

-         Biobase (>= 2.9.0),

-         oligoClasses (>= 1.13.5)

-Imports: affyio (>= 1.15.2),

+         Biobase (>= 2.11.8),

+         oligoClasses (>= 1.13.8)

+Imports: affyio (>= 1.19.2),

          ellipse,

-         ff,

-         genefilter,

+         ff (>= 2.2-1),

+         genefilter (>= 1.33.0),

          mvtnorm,

-         preprocessCore,

+         preprocessCore (>= 1.13.4),

          splines,

          stats,

          SNPchip,

deleted file mode 100644

@@ -1,51 +0,0 @@

-        **************************************************

-        *                                                *

-        *              1.3 SERIES NEWS                   *

-        *                                                *

-        **************************************************

-

-USER VISIBLE CHANGES

-

-     o 3 new classes created:

-

-        i.  'ABset': container for quantile-normalized A and B

-       	    intensities for both SNP and copy number probes.  Required

-       	    assay data elements are 'A' and 'B'.  Extends eSet

-       	    directly.

-

-                - For nonpolymorphic probes, the quantile normalized

-                  intensity is stored in the 'A' assay data element.

-                  The corresponding row in the 'B' assay data element

-                  is NA.  This is a bit inefficient, but greatly

-                  simplifies downstream analyses.  In particular, '['

-                  works.

-

-        ii.  'CrlmmSetList': container for results from preprocessing

-	     and genotyping.  This object is a list.  The first

-	     element of the list is an ABset.  The second element is a

-	     SnpSet containing genotype calls.  The two elements are

-	     required to have identical featureNames and sampleNames.

-

-       		- added several methods for subsetting and accessing

- 		  elements of this object, including featureNames,

- 		  sampleNames, and "[".

-

-         iii. 'CopyNumberSet': contains locus-level estimates of copy

-  	      number for SNPs and polymorphic probes.

-

-       	        - Required assay data elements are 'CA' and 'CB',

-                  corresponding to the absolute copy number for allele

-                  A and B, respectively.

-

-	        - For nonpolymorphic probes, the total copy number is

-                  stored in the 'CA' slot and a NA is recorded for the

-                  corresponding row in the CB matrix. 

-

-		- Useful methods: 'copyNumber', 'ellipse', 'points'

-

-     o 'crlmmWrapper' function does preprocessing

-       (quantile-normalization) and genotyping, saving an object of

-       class CrlmmSetList for each chromosome

-

-     o 'computeCopynumber' now requires an object of class

-        'CrlmmSetList' and returns an object of class 'CopyNumberSet'.