@@ -588,3 +588,4 @@ inside preprocessInfinium2()

 ** ffcolapply() now used instead of ffrowapply()

 ** ff storage only used to initialize callSet - no longer used in storage of RG, XY, res data created along the way (matrices now used here) etc.

 ** removed 'outdir' argument and ldPath() added in 1.9.8

+** verbose argument added to readIdatFiles()

@@ -582,5 +582,9 @@ be used to specify where you want to store the large data objects.  ldPath(outdi

 inside preprocessInfinium2()

 ** the 'batch' variable is now left empty and must be specified by the user

 ** X and Y are now initialized with zeroes by initializeBigMatrix( ,initdata=0) in RGtoXY().

-** open(A(callSet); open(B(callSet) replaces open(callSet) in genotyp.Illumina()

+** open(A(callSet); open(B(callSet) replaces open(callSet) in genotype.Illumina()

+2010-12-10 M. Ritchie 1.9.9

+** ffcolapply() now used instead of ffrowapply()

+** ff storage only used to initialize callSet - no longer used in storage of RG, XY, res data created along the way (matrices now used here) etc.

+** removed 'outdir' argument and ldPath() added in 1.9.8

@@ -576,3 +576,11 @@ function (which expects ff objects and supports parallel processing)

 2010-10-17 M. Ritchie 1.7.22

 **  added "humanomni25quadv1b" to validCdfName() in utils.R and RGtoXY() in crlmm-illumina.R

+2010-11-18 M. Ritchie 1.9.8

+** genotype.Illumina() is now exported and has a man page.  The argument 'outdir' should 

+be used to specify where you want to store the large data objects.  ldPath(outdir) is specified 

+inside preprocessInfinium2()

+** the 'batch' variable is now left empty and must be specified by the user

+** X and Y are now initialized with zeroes by initializeBigMatrix( ,initdata=0) in RGtoXY().

+** open(A(callSet); open(B(callSet) replaces open(callSet) in genotyp.Illumina()

+

@@ -573,3 +573,6 @@ function (which expects ff objects and supports parallel processing)

 2010-10-11 M. Ritchie 1.7.21

 ** fixed bug with indexes for ffrowapply() in genotype.Illumina()

+2010-10-17 M. Ritchie 1.7.22

+**  added "humanomni25quadv1b" to validCdfName() in utils.R and RGtoXY() in crlmm-illumina.R

+

@@ -569,3 +569,7 @@ function (which expects ff objects and supports parallel processing)

 2010-10-07 M. Ritchie 1.7.20

 ** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf

 ** tidied code and added snp.index to ffrowapply() in genotype.Illumina() when calls and confidence values are being updated in callSet.

+

+2010-10-11 M. Ritchie 1.7.21

+** fixed bug with indexes for ffrowapply() in genotype.Illumina()

+

@@ -565,3 +565,7 @@ function (which expects ff objects and supports parallel processing)

 ** new internal function processIDAT which uses ocLapply() to parallelize pre-processing of Illumina data

 ** changes to genotype.Illumina()

 ** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf

+

+2010-10-07 M. Ritchie 1.7.20

+** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf

+** tidied code and added snp.index to ffrowapply() in genotype.Illumina() when calls and confidence values are being updated in callSet.

@@ -561,6 +561,7 @@ function (which expects ff objects and supports parallel processing)

 ** copy number A and B intensities now stored in callSet from genotype.Illumina()

-2010-10-06 M. Ritchie 1.7.18

+2010-10-06 M. Ritchie 1.7.19

 ** new internal function processIDAT which uses ocLapply() to parallelize pre-processing of Illumina data

 ** changes to genotype.Illumina()

+** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf

@@ -559,3 +559,8 @@ function (which expects ff objects and supports parallel processing)

 2010-09-30 M. Ritchie 1.7.16

 ** copy number A and B intensities now stored in callSet from genotype.Illumina()

+

+

+2010-10-06 M. Ritchie 1.7.18

+** new internal function processIDAT which uses ocLapply() to parallelize pre-processing of Illumina data

+** changes to genotype.Illumina()

@@ -556,3 +556,6 @@ function (which expects ff objects and supports parallel processing)

 ** added functions get.ProtocolData.Illumina(), construct.Illumina() and genotype.Illumina() to maintiain consistency with Rob's Affy functions

 ** removed 'save.it', 'load.it', 'snpFile', 'cnFile' arguments from crlmmIllumina(), crlmmIlluminaV2 and preprocessInfinium2().  Updated man pages to reflect these changes.

 ** added a switch so that both regular matrix/ff storage can be handled in each function, depending upon whether the ff package has been loaded.

+

+2010-09-30 M. Ritchie 1.7.16

+** copy number A and B intensities now stored in callSet from genotype.Illumina()

@@ -549,6 +549,10 @@ function (which expects ff objects and supports parallel processing)

 ** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize(). Moved close() statement in preprocessInfinium2()

 ** tidied up crlmm-illumina.R, removing commented out code.

-2010-09-16 M. Ritchie 1.7.13

+2010-09-16 M. Ritchie 1.7.14

 ** added immuno chip 12 as one of the chip options for Illumina.

+2010-09-28 M. Ritchie 1.7.15

+** added functions get.ProtocolData.Illumina(), construct.Illumina() and genotype.Illumina() to maintiain consistency with Rob's Affy functions

+** removed 'save.it', 'load.it', 'snpFile', 'cnFile' arguments from crlmmIllumina(), crlmmIlluminaV2 and preprocessInfinium2().  Updated man pages to reflect these changes.

+** added a switch so that both regular matrix/ff storage can be handled in each function, depending upon whether the ff package has been loaded.

@@ -548,3 +548,7 @@ function (which expects ff objects and supports parallel processing)

 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function

 ** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize(). Moved close() statement in preprocessInfinium2()

 ** tidied up crlmm-illumina.R, removing commented out code.

+

+2010-09-16 M. Ritchie 1.7.13

+** added immuno chip 12 as one of the chip options for Illumina.

+

@@ -546,5 +546,5 @@ function (which expects ff objects and supports parallel processing)

 2010-08-25 M. Ritchie 1.7.12

 ** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina().  These make use of ff objects to store data.

 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function

-** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize().

+** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize(). Moved close() statement in preprocessInfinium2()

 ** tidied up crlmm-illumina.R, removing commented out code.

@@ -546,5 +546,5 @@ function (which expects ff objects and supports parallel processing)

 2010-08-25 M. Ritchie 1.7.12

 ** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina().  These make use of ff objects to store data.

 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function

-** Added a check for whether an object is an 'ff_matrix' before running open() or close() to several functions.  Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize().

+** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize().

 ** tidied up crlmm-illumina.R, removing commented out code.

@@ -546,4 +546,5 @@ function (which expects ff objects and supports parallel processing)

 2010-08-25 M. Ritchie 1.7.12

 ** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina().  These make use of ff objects to store data.

 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function

-** tidied up crlmm-illumina.R, removing commented out code.

\ No newline at end of file

+** Added a check for whether an object is an 'ff_matrix' before running open() or close() to several functions.  Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize().

+** tidied up crlmm-illumina.R, removing commented out code.

@@ -541,4 +541,9 @@ function (which expects ff objects and supports parallel processing)

 ** added omni express 12 as one of the chip options for Illumina.  Also added a check for copy number probes (this chip doesn't have any).

 2010-07-30 R. Scharpf 1.7.8

-** edited construct function for CNSetLM

\ No newline at end of file

+** edited construct function for CNSetLM

+

+2010-08-25 M. Ritchie 1.7.12

+** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina().  These make use of ff objects to store data.

+** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function

+** tidied up crlmm-illumina.R, removing commented out code.

\ No newline at end of file

@@ -539,3 +539,6 @@ function (which expects ff objects and supports parallel processing)

 2010--7-28 M. Ritchie committed version 1.7.7

 ** added omni express 12 as one of the chip options for Illumina.  Also added a check for copy number probes (this chip doesn't have any).

+

+2010-07-30 R. Scharpf 1.7.8

+** edited construct function for CNSetLM

\ No newline at end of file

@@ -536,3 +536,6 @@ function (which expects ff objects and supports parallel processing)

 2010-07-25 M. Ritchie committed version 1.7.6

 ** fixed bug introduced in 1.7.4 by addition of tryCatch() into readIdatFiles().  Thanks to Nolwenn Le Meur for pointing this out.

+

+2010--7-28 M. Ritchie committed version 1.7.7

+** added omni express 12 as one of the chip options for Illumina.  Also added a check for copy number probes (this chip doesn't have any).

@@ -533,3 +533,6 @@ function (which expects ff objects and supports parallel processing)

 2010-05-26 R. Scharpf committed version 1.7.5

 ** minor edits to inst/scripts/copynumber.Rnw

+

+2010-07-25 M. Ritchie committed version 1.7.6

+** fixed bug introduced in 1.7.4 by addition of tryCatch() into readIdatFiles().  Thanks to Nolwenn Le Meur for pointing this out.

@@ -530,3 +530,6 @@ function (which expects ff objects and supports parallel processing)

 2010-05-25 R. Scharpf committed version 1.7.4

 ** wrapped readIDAT in a tryCatch()	   

+

+2010-05-26 R. Scharpf committed version 1.7.5

+** minor edits to inst/scripts/copynumber.Rnw

@@ -522,3 +522,11 @@ function (which expects ff objects and supports parallel processing)

 2010-05-25 R. Scharpf committed version 1.7.2

 ** added example dataset

 ** fixed vignette: inst/scripts/copynumber.Rnw

+

+2010-05-25 R. Scharpf committed version 1.7.3

+** put back in the following check in readIDAT (from r 45050):

+  if(versionNumber<3)

+    stop("Older style IDAT files not supported:  consider updating your scanner settings")

+

+2010-05-25 R. Scharpf committed version 1.7.4

+** wrapped readIDAT in a tryCatch()	   

@@ -519,3 +519,6 @@ function (which expects ff objects and supports parallel processing)

 2010-04-24 B Carvalho committed version 1.7.1

 ** fixed bug in gender prediction that cause a spike in memory usage

+2010-05-25 R. Scharpf committed version 1.7.2

+** added example dataset

+** fixed vignette: inst/scripts/copynumber.Rnw

@@ -516,4 +516,6 @@ function (which expects ff objects and supports parallel processing)

 2010-04-16 B Carvalho committed version 1.5.49

 ** cosmetics - looking for cause of memory spike

+2010-04-24 B Carvalho committed version 1.7.1

+** fixed bug in gender prediction that cause a spike in memory usage

@@ -513,5 +513,7 @@ function (which expects ff objects and supports parallel processing)

 2010-04-11 R. Scharpf committed version 1.5.48

 ** added a few .Rd files

+2010-04-16 B Carvalho committed version 1.5.49

+** cosmetics - looking for cause of memory spike

@@ -509,3 +509,9 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 ** crlmmIllumina2() and crlmmIlluminaV2() now use the crlmmGT2() 

 function (which expects ff objects and supports parallel processing)

 ** updated crlmmIllumina.pdf vignette

+

+2010-04-11 R. Scharpf committed version 1.5.48

+** added a few .Rd files

+

+

+

@@ -501,5 +501,11 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 ** modified the storage of RG, XY and genotype call data to use the ff package and initializeBigMatrix() function from oligoClasses package.  The genotype call data now includes non-polymorphic probes (which have NA calls).  Functions which use ff storage are named readIdatFiles2(), RGtoXY2(), preprocessInfinium2v2(), crlmmIllumina2() and crlmmIlluminaV2().

 2010-04-08 B Carvalho committed version 1.5.46

-

 ** moved NEWS to inst/

+

+2010-04-09 M. Ritchie committed version 1.5.47

+** fixed bugs in code and removed copy number probes from output 

+(now saved separately as before - SnpSuperSet not used)

+** crlmmIllumina2() and crlmmIlluminaV2() now use the crlmmGT2() 

+function (which expects ff objects and supports parallel processing)

+** updated crlmmIllumina.pdf vignette

@@ -499,3 +499,7 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 2010-04-07 M. Ritchie committed version 1.5.45

 ** modified the storage of RG, XY and genotype call data to use the ff package and initializeBigMatrix() function from oligoClasses package.  The genotype call data now includes non-polymorphic probes (which have NA calls).  Functions which use ff storage are named readIdatFiles2(), RGtoXY2(), preprocessInfinium2v2(), crlmmIllumina2() and crlmmIlluminaV2().

+

+2010-04-08 B Carvalho committed version 1.5.46

+

+** moved NEWS to inst/

@@ -496,3 +496,6 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

    with crlmm2

 ** added crlmmCopynumber2 for parallel support with copy number

    est. (needs more checking)

+

+2010-04-07 M. Ritchie committed version 1.5.45

+** modified the storage of RG, XY and genotype call data to use the ff package and initializeBigMatrix() function from oligoClasses package.  The genotype call data now includes non-polymorphic probes (which have NA calls).  Functions which use ff storage are named readIdatFiles2(), RGtoXY2(), preprocessInfinium2v2(), crlmmIllumina2() and crlmmIlluminaV2().

@@ -489,3 +489,10 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 ** added parallel/large dataset support to snprma/crlmm

 ** merged changes on .41 with my local changes

+

+2010-04-01 R.Scharpf committed version 1.5.44

+

+** added functions genotype2, cnrma2 for preprocessing and genotyping

+   with crlmm2

+** added crlmmCopynumber2 for parallel support with copy number

+   est. (needs more checking)

@@ -485,3 +485,7 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 ** updates to genotype, crlmmIlluminaRS, crlmmCopynumber

 ** class union of ff_matrix, matrix, and ffdf

+2010-03-18 B Carvalho committed version 1.5.42

+

+** added parallel/large dataset support to snprma/crlmm

+** merged changes on .41 with my local changes

@@ -478,9 +478,10 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 ** a few updates to initializeBigMatrix

 ** show, [ defined for CNSetLM

-2010-03-18 R.Scharpf committed version 1.5.38

+2010-03-25 R.Scharpf committed version 1.5.41

 ** import snpCall, snpCallProbability, snpCall<-, snpCallProbability<-

    from Biobase

-** updates to genotype and crlmmIlluminaRS

+** updates to genotype, crlmmIlluminaRS, crlmmCopynumber

 ** class union of ff_matrix, matrix, and ffdf

+

@@ -477,3 +477,10 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 ** a few updates to initializeBigMatrix

 ** show, [ defined for CNSetLM

+

+2010-03-18 R.Scharpf committed version 1.5.38

+

+** import snpCall, snpCallProbability, snpCall<-, snpCallProbability<-

+   from Biobase

+** updates to genotype and crlmmIlluminaRS

+** class union of ff_matrix, matrix, and ffdf

@@ -473,3 +473,7 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

      (currently saving intermediate steps in crlmmIlluminaRS)

      removed cnOptions function and changed arguments to crlmmCopynumber

+2010-03-18 R.Scharpf committed version 1.5.38

+

+** a few updates to initializeBigMatrix

+** show, [ defined for CNSetLM

@@ -467,3 +467,9 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 **   added crlmmIlluminaRS to cnrma-functions.R (testing)

+2010-03-18 R.Scharpf committed version 1.5.37

+

+**   fixed bugs in genotype() and crlmmIlluminaRS.

+     (currently saving intermediate steps in crlmmIlluminaRS)

+     removed cnOptions function and changed arguments to crlmmCopynumber

+

@@ -416,19 +416,29 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 2010-03-07 R. Scharpf committed version 1.5.30

-- one can use ff in conjunction with affy platforms 5.0 and 6.0

-

-- more s4-style code

-

-- preprocessing / genotyping is basically the same set of commands with either illumina/affy platforms (though illumina-users may have to play with some of the options for reading idat files

-

-- if ff package is loaded, the assayData elements are ff objects

-

-- the classes all inherit from 'CrlmmContainer' that contains an additional slot 'options' and 'genomeAnnotation'.   options is a list with the default arguments to snprma, crlmm, etc, as well as a few global settings such as 'verbose' and 'seed'.  I added the genomeAnnotation slot simply because I want to be able to use ff-objects for the feature-level data.   Maybe with setClassUnion we could avoid adding the genomeAnnotation slot (and use featureData instead), but I didn't have much success with this.

-

-- the batchSize argument will run the genotyping (crlmmGT) in batches to reduce the RAM.  The default is batches of size 1000.

-

-- The crlmm.Rd file contains an example with / without ff for Affymetrix data.

+       - one can use ff in conjunction with affy platforms 5.0 and 6.0

+       - preprocessing / genotyping is basically the same set of

+        commands with either illumina/affy platforms (though

+        illumina-users may have to play with some of the options for

+        reading idat files

+       - if ff package is loaded, the assayData elements are ff objects

+

+       - the classes all inherit from 'CrlmmContainer' that contains

+         an additional slot 'options' and 'genomeAnnotation'.  options

+         is a list with the default arguments to snprma, crlmm, etc,

+         as well as a few global settings such as 'verbose' and

+         'seed'.  I added the genomeAnnotation slot simply because I

+         want to be able to use ff-objects for the feature-level data.

+         Maybe with setClassUnion we could avoid adding the

+         genomeAnnotation slot (and use featureData instead), but I

+         didn't have much success with this.

+

+	 - the batchSize argument will run the genotyping (crlmmGT) in

+           batches to reduce the RAM.  The default is batches of size

+           1000.

+

+	 - The crlmm.Rd file contains an example with / without ff

+             for Affymetrix data.

 2010-03-08 M. Ritchie committed version 1.5.31

  * removed a few unnecessary lines of code from crlmm-illumina.R (zero not needed as argument for preprocessInfinium2() and storageMode should not be "lockedEnvironment" in RGtoXY()) 

@@ -436,7 +446,7 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 2010-03-08 R.Scharpf committed version 1.5.32

-**	   This is a roll back to version 1.5.24 

+**	   Rolled back to version 1.5.24 

 2010-03-08 R.Scharpf committed version 1.5.33

@@ -447,3 +457,13 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 **	  updated DESCRIPTION to import ff

 **        added AllClasses.R with defitions for ff-derived classes

 **        temporarily exporting everything in the NAMESPACE

+

+2010-03-11 R.Scharpf committed version 1.5.35

+

+**        added genotype() in cnrma-functions -- for preprocessing and

+          genotyping affy

+

+2010-03-14 R.Scharpf committed version 1.5.36

+

+**   added crlmmIlluminaRS to cnrma-functions.R (testing)

+

@@ -441,3 +441,9 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 2010-03-08 R.Scharpf committed version 1.5.33

 **	  Added annotatedDataFrameFrom methods for ff_matrix and ffdf (in utils)

+

+2010-03-10 R.Scharpf committed version 1.5.34

+

+**	  updated DESCRIPTION to import ff

+**        added AllClasses.R with defitions for ff-derived classes

+**        temporarily exporting everything in the NAMESPACE

@@ -438,4 +438,6 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 **	   This is a roll back to version 1.5.24 

+2010-03-08 R.Scharpf committed version 1.5.33

+**	  Added annotatedDataFrameFrom methods for ff_matrix and ffdf (in utils)

@@ -433,3 +433,9 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 2010-03-08 M. Ritchie committed version 1.5.31

  * removed a few unnecessary lines of code from crlmm-illumina.R (zero not needed as argument for preprocessInfinium2() and storageMode should not be "lockedEnvironment" in RGtoXY()) 

  * added "humanomni1quadv1b" to validCdfName() in utils.R

+

+2010-03-08 R.Scharpf committed version 1.5.32

+

+**	   This is a roll back to version 1.5.24 

+	   

+

@@ -429,3 +429,7 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 - the batchSize argument will run the genotyping (crlmmGT) in batches to reduce the RAM.  The default is batches of size 1000.

 - The crlmm.Rd file contains an example with / without ff for Affymetrix data.

+

+2010-03-08 M. Ritchie committed version 1.5.31

+ * removed a few unnecessary lines of code from crlmm-illumina.R (zero not needed as argument for preprocessInfinium2() and storageMode should not be "lockedEnvironment" in RGtoXY()) 

+ * added "humanomni1quadv1b" to validCdfName() in utils.R

@@ -413,3 +413,19 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

 2010-03-05 M. Ritchie - committed version 1.5.29

  * crlmmIlluminaV2() now exported.  Added man page crlmmIlluminaV2.Rd

+

+2010-03-07 R. Scharpf committed version 1.5.30

+

+- one can use ff in conjunction with affy platforms 5.0 and 6.0

+

+- more s4-style code

+

+- preprocessing / genotyping is basically the same set of commands with either illumina/affy platforms (though illumina-users may have to play with some of the options for reading idat files

+

+- if ff package is loaded, the assayData elements are ff objects

+

+- the classes all inherit from 'CrlmmContainer' that contains an additional slot 'options' and 'genomeAnnotation'.   options is a list with the default arguments to snprma, crlmm, etc, as well as a few global settings such as 'verbose' and 'seed'.  I added the genomeAnnotation slot simply because I want to be able to use ff-objects for the feature-level data.   Maybe with setClassUnion we could avoid adding the genomeAnnotation slot (and use featureData instead), but I didn't have much success with this.

+

+- the batchSize argument will run the genotyping (crlmmGT) in batches to reduce the RAM.  The default is batches of size 1000.

+

+- The crlmm.Rd file contains an example with / without ff for Affymetrix data.

@@ -410,3 +410,6 @@ Such files arise when scanner settings contain the line <GenerateVersionTwoIdatF

 If this is modified to <GenerateVersionTwoIdatFiles>true</GenerateVersionTwoIdatFiles>, 

 then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

  * Removed AllClasses.R from Collate field in DESCRIPTION file (causes an error in build)

+

+2010-03-05 M. Ritchie - committed version 1.5.29

+ * crlmmIlluminaV2() now exported.  Added man page crlmmIlluminaV2.Rd

@@ -386,7 +386,7 @@ is stored in the assayData slot.

 2010-02-07 B. Carvalho - committed version 1.5.25

  * Updated requirement of affyio to support Win64

-2010-02-20 R. Scharpf - committed version 1.5.25

+2010-02-20 R. Scharpf - committed version 1.5.26

 ** begin adding support for ff

@@ -400,8 +400,13 @@ is stored in the assayData slot.

       - B.rda

       - cn_rmaResult.rda (SKW)

-2010-02-21 R. Scharpf - committed version 1.5.26

+2010-02-21 R. Scharpf - committed version 1.5.27

 ** additional support for ff in crlmm and computeCopynumber functions

-

+2010-03-02 M. Ritchie - committed version 1.5.28

+ * Added message to readIDAT() warning that older style IDAT files can not be read in.

+Such files arise when scanner settings contain the line <GenerateVersionTwoIdatFiles>false</GenerateVersionTwoIdatFiles>

+If this is modified to <GenerateVersionTwoIdatFiles>true</GenerateVersionTwoIdatFiles>, 

+then readIDAT() should work. Thanks to Pierre Cherel who reported this error.

+ * Removed AllClasses.R from Collate field in DESCRIPTION file (causes an error in build)

@@ -400,4 +400,8 @@ is stored in the assayData slot.

       - B.rda

       - cn_rmaResult.rda (SKW)

+2010-02-21 R. Scharpf - committed version 1.5.26

+ 

+** additional support for ff in crlmm and computeCopynumber functions

+

@@ -385,3 +385,19 @@ is stored in the assayData slot.

 2010-02-07 B. Carvalho - committed version 1.5.25

  * Updated requirement of affyio to support Win64

+

+2010-02-20 R. Scharpf - committed version 1.5.25

+

+** begin adding support for ff

+

+** added use.poe option for nonpolymorphic loci

+

+** crlmm does not return anything, but saves the following objects:

+      - genotypes.rda

+      - confs.rda

+      - snp_rmaResult.rda  (gns, sns, SNR, SKW, mixtureParams, cdfName)

+      - A.rda

+      - B.rda

+      - cn_rmaResult.rda (SKW)

+

+

@@ -382,3 +382,6 @@ is stored in the assayData slot.

 2010-02-05 M. Ritchie - committed version 1.5.24

  * preprocessed allele A and B intensities from copy number and regular SNPs are now saved separately by crlmmIllumina().  The 'intensityFile' argument has been replaced by 'snpFile' and 'cnFile'.

  * updated the following man pages to reflect the above changes and added in current references:  crlmmIllumina.Rd, crlmm.Rd and readIdatFiles.Rd

+

+2010-02-07 B. Carvalho - committed version 1.5.25

+ * Updated requirement of affyio to support Win64

@@ -377,7 +377,8 @@ in the one function to reduce memory usage (not exported as yet)

 to save memory.  Instead, 'zero', which indicates which SNPs have zero beads 

 is stored in the assayData slot.

  * now store 'zero' with copy number AB intensities in preprocessInfinium2()

+ * deleted man pages crlmm.Rd and readIdatFiles.Rd added back

 2010-02-05 M. Ritchie - committed version 1.5.24

  * preprocessed allele A and B intensities from copy number and regular SNPs are now saved separately by crlmmIllumina().  The 'intensityFile' argument has been replaced by 'snpFile' and 'cnFile'.

- * updated man page for crlmmIllumina()

\ No newline at end of file

+ * updated the following man pages to reflect the above changes and added in current references:  crlmmIllumina.Rd, crlmm.Rd and readIdatFiles.Rd

@@ -377,3 +377,7 @@ in the one function to reduce memory usage (not exported as yet)

 to save memory.  Instead, 'zero', which indicates which SNPs have zero beads 

 is stored in the assayData slot.

  * now store 'zero' with copy number AB intensities in preprocessInfinium2()

+

+2010-02-05 M. Ritchie - committed version 1.5.24

+ * preprocessed allele A and B intensities from copy number and regular SNPs are now saved separately by crlmmIllumina().  The 'intensityFile' argument has been replaced by 'snpFile' and 'cnFile'.

+ * updated man page for crlmmIllumina()

\ No newline at end of file

@@ -363,9 +363,17 @@ is decoded and scanned

  * Added 'humanomni1quadv1b" to chip types allowed in RGtoXY()

-

 2010-01-20 R. Scharpf - committed version 1.5.21

  * Added CopyNumberVariants to DESCRIPTION

 2010-01-20 R. Scharpf - committed version 1.5.22

  * restored inst/doc/crlmmDownstream.Rnw

+

+2010-02-04 M. Ritchie - committed version 1.5.23

+ * crlmmIllumina now exported in NAMESPACE (removed at some point)

+ * new function crlmmIlluminaV2() which reads in .idats and genotypes 

+in the one function to reduce memory usage (not exported as yet)

+ * readIdatFiles() modified to no longer store number of beads and beads SE

+to save memory.  Instead, 'zero', which indicates which SNPs have zero beads 

+is stored in the assayData slot.

+ * now store 'zero' with copy number AB intensities in preprocessInfinium2()

@@ -366,3 +366,6 @@ is decoded and scanned

 2010-01-20 R. Scharpf - committed version 1.5.21

  * Added CopyNumberVariants to DESCRIPTION

+

+2010-01-20 R. Scharpf - committed version 1.5.22

+ * restored inst/doc/crlmmDownstream.Rnw

@@ -362,3 +362,7 @@ is decoded and scanned

 2009-12-24 M. Ritchie - committed version 1.5.19

  * Added 'humanomni1quadv1b" to chip types allowed in RGtoXY()

+

+

+2010-01-20 R. Scharpf - committed version 1.5.21

+ * Added CopyNumberVariants to DESCRIPTION

@@ -181,7 +181,7 @@ is decoded and scanned

 2009-07-01 M Ritchie - committed version 1.3.7

-* made memory savings to reading and normalization if Illumina data

+* made memory savings to reading and normalization of Illumina data

 * Now use 'protocolData' slot to save scan dates instead of saving them in phenoData slot

 * added vignette for genoytping illumina data (crlmmIllumina.pdf in inst/doc and crlmmIllumina.Rnw in inst/scripts)

 * Changed stop() to warning() when idats are of different type in readIdatFiles()

@@ -351,11 +351,14 @@ is decoded and scanned

  * moved IRanges and oligoClasses to Depends (DESCRIPTION)

-2009-12-23 R. Scharpf - commited version 1.5.17

+2009-12-23 R. Scharpf - committed version 1.5.17

 ** updated first half of inst/scripts/copynumber.Rnw, as well as a few of the help files

-2009-12-23 R. Scharpf - commited version 1.5.18

+2009-12-23 R. Scharpf - committed version 1.5.18

 ** removed generics for addFeatureAnnotation and GT<-

+2009-12-24 M. Ritchie - committed version 1.5.19

+

+ * Added 'humanomni1quadv1b" to chip types allowed in RGtoXY()

@@ -354,3 +354,8 @@ is decoded and scanned

 2009-12-23 R. Scharpf - commited version 1.5.17

 ** updated first half of inst/scripts/copynumber.Rnw, as well as a few of the help files

+

+2009-12-23 R. Scharpf - commited version 1.5.18

+

+** removed generics for addFeatureAnnotation and GT<-

+

@@ -350,3 +350,7 @@ is decoded and scanned

 2009-12-04 B. Carvalho - committed version 1.5.11

  * moved IRanges and oligoClasses to Depends (DESCRIPTION)

+

+2009-12-23 R. Scharpf - commited version 1.5.17

+

+** updated first half of inst/scripts/copynumber.Rnw, as well as a few of the help files

@@ -346,3 +346,7 @@ is decoded and scanned

       removed inadvertantly in version 1.3.7, put back]

  * removed header checking from readIdatFiles() (seems to fail often).  

       Instead check that the number of SNPs agrees (to within +/- 10K SNPs)

+

+2009-12-04 B. Carvalho - committed version 1.5.11

+

+ * moved IRanges and oligoClasses to Depends (DESCRIPTION)

@@ -344,3 +344,5 @@ is decoded and scanned

  * bug fixed in stripNormalize() [X+16,Y+16 which avoids log(0) = -Inf values, 

       removed inadvertantly in version 1.3.7, put back]

+ * removed header checking from readIdatFiles() (seems to fail often).  

+      Instead check that the number of SNPs agrees (to within +/- 10K SNPs)

@@ -340,3 +340,7 @@ is decoded and scanned

  * fixed bugs in addFeatureAnnotation.SnpCallSetPlus

+2009-12-01 M. Ritchie - committed version 1.5.8

+

+ * bug fixed in stripNormalize() [X+16,Y+16 which avoids log(0) = -Inf values, 

+      removed inadvertantly in version 1.3.7, put back]

@@ -332,7 +332,11 @@ is decoded and scanned

  * added CNSet class

  * segmentData slot in CNSet class is an extension of RangedData (defined in IRanges package)

-2009-11-19 R. Scharpf - committed version 1.5.6

+2009-11-19 R. Scharpf - committed version 1.5.6 

- * fixed bug in initialization of SnpCallSetPlus

+ * fixed bugs in initialization of SnpCallSetPlus

+

+2009-11-19 R. Scharpf - committed version 1.5.7

+

+ * fixed bugs in addFeatureAnnotation.SnpCallSetPlus

@@ -332,3 +332,7 @@ is decoded and scanned

  * added CNSet class

  * segmentData slot in CNSet class is an extension of RangedData (defined in IRanges package)

+2009-11-19 R. Scharpf - committed version 1.5.6

+

+ * fixed bug in initialization of SnpCallSetPlus

+

@@ -326,3 +326,9 @@ is decoded and scanned

  * fixed classes imported from oligoClasses in NAMESPACE

  * imported 'calls<-' from oligoClasses

+2009-11-19 R. Scharpf - committed version 1.5.5

+

+ * removed a few of the classes (CrlmmSet, CrlmmSetFF, SnpCallSetPlusFF,...)

+ * added CNSet class

+ * segmentData slot in CNSet class is an extension of RangedData (defined in IRanges package)

+

@@ -319,4 +319,10 @@ is decoded and scanned

  - ABset and CrlmmSetList classes are gone. Using SnpCallSetPlus and CrlmmSet

  - Added class SegmentSet that extends CrlmmSet directly.

+2009-11-15 B Carvalho - committed version 1.5.4

+

+ * removed references to old C code

+ * added the missing files to the Collate field

+ * fixed classes imported from oligoClasses in NAMESPACE

+ * imported 'calls<-' from oligoClasses

@@ -312,3 +312,11 @@ is decoded and scanned

 2009-11-14 B Carvalho - committed version 1.5.2

  * code cleanup - removed unneeded C code

+

+2009-11-15 R. Scharpf - committed version 1.5.3

+

+ * numerous changes to the copy number estimation

+ - ABset and CrlmmSetList classes are gone. Using SnpCallSetPlus and CrlmmSet

+ - Added class SegmentSet that extends CrlmmSet directly.

+

+

@@ -308,3 +308,7 @@ is decoded and scanned

  * fixed bug in readIdatFiles()

  * updated crlmmIllumina.Rnw and crlmmIllumina.pdf

+

+2009-11-14 B Carvalho - committed version 1.5.2

+

+ * code cleanup - removed unneeded C code

@@ -303,5 +303,8 @@ is decoded and scanned

  * updated illumina_copynumber vignette

+2009-10-25 M Ritchie - committed version 1.3.24

+ * fixed bug in readIdatFiles()

+ * updated crlmmIllumina.Rnw and crlmmIllumina.pdf

@@ -290,3 +290,18 @@ is decoded and scanned

 * updated addFeatureAnnotation so that CHR arg not required

 * fixed bug in nonpolymorphic function -- function checks whether any regions are pseudoautosomal 

 * fixed bug in list2locusset function (no longer assigns genomewidesnp6 as the default annotation)

+

+2009-10-16 R. Scharpf - committed version 1.3.23

+

+ * 100*CA, 100*CB are stored in the CA, CB assayDataElements.  The

+   replacement method automatically converts a matrix on the copy

+   number scale to an integer representation by scaling by a factor of

+   100. The accessor methods for CA, CB automatically divide by 100 to

+   return estimates back on the original copy number scale.

+

+ * more debugging of readIdatFiles and illumina copy number vignette.

+

+ * updated illumina_copynumber vignette

+

+

+

@@ -282,3 +282,11 @@ is decoded and scanned

 * changed copyNumber() method so that CA + NA = NA, CB + NA = NA (previously had CA+NA=CA, but this can result in a lot of zeros, depending on the genotype)

 * new method: addFeatureAnnotation

 * support for snp5.0

+

+2009-10-04 R. Scharpf - committed version 1.3.22

+

+* changed default path argument for readIdatFiles to empty quotes

+* fixed bug in update method for character strings

+* updated addFeatureAnnotation so that CHR arg not required

+* fixed bug in nonpolymorphic function -- function checks whether any regions are pseudoautosomal 

+* fixed bug in list2locusset function (no longer assigns genomewidesnp6 as the default annotation)

@@ -272,3 +272,13 @@ is decoded and scanned

 * labeled figures / displayed output of code chunks in the copy number vignette

 * added bibliography for copy number vignette.  Added file inst/doc/refs.bib

 * added boxplot method 

+

+2009-10-03 R. Scharpf - committed version 1.3.21

+

+* modified crlmmWrapper function

+* modified illumina copy number vignette (still needs debugging)

+* changed title of copy number vignette

+* added reference to the crlmm paper

+* changed copyNumber() method so that CA + NA = NA, CB + NA = NA (previously had CA+NA=CA, but this can result in a lot of zeros, depending on the genotype)

+* new method: addFeatureAnnotation

+* support for snp5.0

@@ -264,3 +264,11 @@ is decoded and scanned

 * overhaul of vignette

 * added update() method for copy number

 * added documentation and error checks for crlmmWrapper

+

+2009-08-14 R. Scharpf - committed version 1.3.19

+

+* changes to crlmmWrapper (trying to make this handle the illumina platform as well...still needs testing)

+  - removed crlmmIlluminaWrapper.Rd, and commented crlmmIlluminaWrapper function

+* labeled figures / displayed output of code chunks in the copy number vignette

+* added bibliography for copy number vignette.  Added file inst/doc/refs.bib