Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@51434 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 09/12/2010 17:33:50
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@@ -588,3 +588,4 @@ inside preprocessInfinium2()
588 588
 ** ffcolapply() now used instead of ffrowapply()
589 589
 ** 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.
590 590
 ** removed 'outdir' argument and ldPath() added in 1.9.8
591
+** verbose argument added to readIdatFiles()
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@51433 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 09/12/2010 17:33:21
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@@ -582,5 +582,9 @@ be used to specify where you want to store the large data objects.  ldPath(outdi
582 582
 inside preprocessInfinium2()
583 583
 ** the 'batch' variable is now left empty and must be specified by the user
584 584
 ** X and Y are now initialized with zeroes by initializeBigMatrix( ,initdata=0) in RGtoXY().
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-** open(A(callSet); open(B(callSet) replaces open(callSet) in genotyp.Illumina()
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+** open(A(callSet); open(B(callSet) replaces open(callSet) in genotype.Illumina()
586 586
 
587
+2010-12-10 M. Ritchie 1.9.9
588
+** ffcolapply() now used instead of ffrowapply()
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+** 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.
590
+** removed 'outdir' argument and ldPath() added in 1.9.8
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50950 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 18/11/2010 05:31:36
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@@ -576,3 +576,11 @@ function (which expects ff objects and supports parallel processing)
576 576
 2010-10-17 M. Ritchie 1.7.22
577 577
 **  added "humanomni25quadv1b" to validCdfName() in utils.R and RGtoXY() in crlmm-illumina.R
578 578
 
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+2010-11-18 M. Ritchie 1.9.8
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+** genotype.Illumina() is now exported and has a man page.  The argument 'outdir' should 
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+be used to specify where you want to store the large data objects.  ldPath(outdir) is specified 
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+inside preprocessInfinium2()
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+** the 'batch' variable is now left empty and must be specified by the user
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+** X and Y are now initialized with zeroes by initializeBigMatrix( ,initdata=0) in RGtoXY().
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+** open(A(callSet); open(B(callSet) replaces open(callSet) in genotyp.Illumina()
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+
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50264 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 16/10/2010 13:23:54
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@@ -573,3 +573,6 @@ function (which expects ff objects and supports parallel processing)
573 573
 2010-10-11 M. Ritchie 1.7.21
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 ** fixed bug with indexes for ffrowapply() in genotype.Illumina()
575 575
 
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+2010-10-17 M. Ritchie 1.7.22
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+**  added "humanomni25quadv1b" to validCdfName() in utils.R and RGtoXY() in crlmm-illumina.R
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+
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50078 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 10/10/2010 23:05:18
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@@ -569,3 +569,7 @@ function (which expects ff objects and supports parallel processing)
569 569
 2010-10-07 M. Ritchie 1.7.20
570 570
 ** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf
571 571
 ** tidied code and added snp.index to ffrowapply() in genotype.Illumina() when calls and confidence values are being updated in callSet.
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+
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+2010-10-11 M. Ritchie 1.7.21
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+** fixed bug with indexes for ffrowapply() in genotype.Illumina()
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+
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50021 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 08/10/2010 04:45:17
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@@ -565,3 +565,7 @@ function (which expects ff objects and supports parallel processing)
565 565
 ** new internal function processIDAT which uses ocLapply() to parallelize pre-processing of Illumina data
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 ** changes to genotype.Illumina()
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 ** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf
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+
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+2010-10-07 M. Ritchie 1.7.20
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+** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf
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+** tidied code and added snp.index to ffrowapply() in genotype.Illumina() when calls and confidence values are being updated in callSet.
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49990 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 07/10/2010 07:22:57
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@@ -561,6 +561,7 @@ function (which expects ff objects and supports parallel processing)
561 561
 ** copy number A and B intensities now stored in callSet from genotype.Illumina()
562 562
 
563 563
 
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-2010-10-06 M. Ritchie 1.7.18
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+2010-10-06 M. Ritchie 1.7.19
565 565
 ** new internal function processIDAT which uses ocLapply() to parallelize pre-processing of Illumina data
566 566
 ** changes to genotype.Illumina()
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+** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49966 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 06/10/2010 07:28:28
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@@ -559,3 +559,8 @@ function (which expects ff objects and supports parallel processing)
559 559
 
560 560
 2010-09-30 M. Ritchie 1.7.16
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 ** copy number A and B intensities now stored in callSet from genotype.Illumina()
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+
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+
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+2010-10-06 M. Ritchie 1.7.18
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+** new internal function processIDAT which uses ocLapply() to parallelize pre-processing of Illumina data
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+** changes to genotype.Illumina()
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49718 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 30/09/2010 01:06:00
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@@ -556,3 +556,6 @@ function (which expects ff objects and supports parallel processing)
556 556
 ** added functions get.ProtocolData.Illumina(), construct.Illumina() and genotype.Illumina() to maintiain consistency with Rob's Affy functions
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 ** removed 'save.it', 'load.it', 'snpFile', 'cnFile' arguments from crlmmIllumina(), crlmmIlluminaV2 and preprocessInfinium2().  Updated man pages to reflect these changes.
558 558
 ** 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.
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+
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+2010-09-30 M. Ritchie 1.7.16
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+** copy number A and B intensities now stored in callSet from genotype.Illumina()
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49660 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 28/09/2010 01:44:41
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@@ -549,6 +549,10 @@ function (which expects ff objects and supports parallel processing)
549 549
 ** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize(). Moved close() statement in preprocessInfinium2()
550 550
 ** tidied up crlmm-illumina.R, removing commented out code.
551 551
 
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-2010-09-16 M. Ritchie 1.7.13
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+2010-09-16 M. Ritchie 1.7.14
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 ** added immuno chip 12 as one of the chip options for Illumina.
554 554
 
555
+2010-09-28 M. Ritchie 1.7.15
556
+** added functions get.ProtocolData.Illumina(), construct.Illumina() and genotype.Illumina() to maintiain consistency with Rob's Affy functions
557
+** removed 'save.it', 'load.it', 'snpFile', 'cnFile' arguments from crlmmIllumina(), crlmmIlluminaV2 and preprocessInfinium2().  Updated man pages to reflect these changes.
558
+** 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.
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49420 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 16/09/2010 12:01:16
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@@ -548,3 +548,7 @@ function (which expects ff objects and supports parallel processing)
548 548
 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function
549 549
 ** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize(). Moved close() statement in preprocessInfinium2()
550 550
 ** tidied up crlmm-illumina.R, removing commented out code.
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+
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+2010-09-16 M. Ritchie 1.7.13
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+** added immuno chip 12 as one of the chip options for Illumina.
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+
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49035 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 25/08/2010 23:53:32
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@@ -546,5 +546,5 @@ function (which expects ff objects and supports parallel processing)
546 546
 2010-08-25 M. Ritchie 1.7.12
547 547
 ** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina().  These make use of ff objects to store data.
548 548
 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function
549
-** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize().
549
+** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize(). Moved close() statement in preprocessInfinium2()
550 550
 ** tidied up crlmm-illumina.R, removing commented out code.
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49013 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 25/08/2010 05:08:54
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@@ -546,5 +546,5 @@ function (which expects ff objects and supports parallel processing)
546 546
 2010-08-25 M. Ritchie 1.7.12
547 547
 ** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina().  These make use of ff objects to store data.
548 548
 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function
549
-** 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().
549
+** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize().
550 550
 ** tidied up crlmm-illumina.R, removing commented out code.
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49012 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 25/08/2010 04:07:29
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@@ -546,4 +546,5 @@ function (which expects ff objects and supports parallel processing)
546 546
 2010-08-25 M. Ritchie 1.7.12
547 547
 ** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina().  These make use of ff objects to store data.
548 548
 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function
549
-** tidied up crlmm-illumina.R, removing commented out code.
550 549
\ No newline at end of file
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+** 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().
551
+** tidied up crlmm-illumina.R, removing commented out code.
Browse code

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
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@@ -541,4 +541,9 @@ function (which expects ff objects and supports parallel processing)
541 541
 ** 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).
542 542
 
543 543
 2010-07-30 R. Scharpf 1.7.8
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-** edited construct function for CNSetLM
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\ No newline at end of file
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+** edited construct function for CNSetLM
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+
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+2010-08-25 M. Ritchie 1.7.12
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+** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina().  These make use of ff objects to store data.
549
+** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function
550
+** tidied up crlmm-illumina.R, removing commented out code.
546 551
\ No newline at end of file
Browse code

v 1.7.8 updated changes/description

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48621 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 02/08/2010 08:51:59
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@@ -539,3 +539,6 @@ function (which expects ff objects and supports parallel processing)
539 539
 
540 540
 2010--7-28 M. Ritchie committed version 1.7.7
541 541
 ** 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).
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+
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+2010-07-30 R. Scharpf 1.7.8
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+** edited construct function for CNSetLM
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\ No newline at end of file
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48480 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 28/07/2010 02:03:14
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@@ -536,3 +536,6 @@ function (which expects ff objects and supports parallel processing)
536 536
 
537 537
 2010-07-25 M. Ritchie committed version 1.7.6
538 538
 ** fixed bug introduced in 1.7.4 by addition of tryCatch() into readIdatFiles().  Thanks to Nolwenn Le Meur for pointing this out.
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+
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+2010--7-28 M. Ritchie committed version 1.7.7
541
+** 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).
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48398 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 25/07/2010 04:42:43
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@@ -533,3 +533,6 @@ function (which expects ff objects and supports parallel processing)
533 533
 
534 534
 2010-05-26 R. Scharpf committed version 1.7.5
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 ** minor edits to inst/scripts/copynumber.Rnw
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+2010-07-25 M. Ritchie committed version 1.7.6
538
+** fixed bug introduced in 1.7.4 by addition of tryCatch() into readIdatFiles().  Thanks to Nolwenn Le Meur for pointing this out.
Browse code

minor edits to copynumber.Rnw

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@47206 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 29/05/2010 03:30:32
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@@ -530,3 +530,6 @@ function (which expects ff objects and supports parallel processing)
530 530
 
531 531
 2010-05-25 R. Scharpf committed version 1.7.4
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 ** wrapped readIDAT in a tryCatch()	   
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+2010-05-26 R. Scharpf committed version 1.7.5
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+** minor edits to inst/scripts/copynumber.Rnw
Browse code

wrapped readIDAT in a tryCatch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@47129 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 25/05/2010 19:20:33
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@@ -522,3 +522,11 @@ function (which expects ff objects and supports parallel processing)
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 2010-05-25 R. Scharpf committed version 1.7.2
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 ** added example dataset
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 ** fixed vignette: inst/scripts/copynumber.Rnw
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+2010-05-25 R. Scharpf committed version 1.7.3
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+** put back in the following check in readIDAT (from r 45050):
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+  if(versionNumber<3)
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+    stop("Older style IDAT files not supported:  consider updating your scanner settings")
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+
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+2010-05-25 R. Scharpf committed version 1.7.4
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+** wrapped readIDAT in a tryCatch()	   
Browse code

updated copynumber vignette in inst/scripts. Added example datasets

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@47121 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 25/05/2010 13:07:43
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@@ -519,3 +519,6 @@ function (which expects ff objects and supports parallel processing)
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 2010-04-24 B Carvalho committed version 1.7.1
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 ** fixed bug in gender prediction that cause a spike in memory usage
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+2010-05-25 R. Scharpf committed version 1.7.2
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+** added example dataset
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+** fixed vignette: inst/scripts/copynumber.Rnw
Browse code

Fixed problem with memory management

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@46584 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 27/04/2010 14:40:30
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@@ -516,4 +516,6 @@ function (which expects ff objects and supports parallel processing)
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 2010-04-16 B Carvalho committed version 1.5.49
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 ** cosmetics - looking for cause of memory spike
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+2010-04-24 B Carvalho committed version 1.7.1
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+** fixed bug in gender prediction that cause a spike in memory usage
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Browse code

Started debugging - memory spike

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@46099 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 16/04/2010 16:02:49
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@@ -513,5 +513,7 @@ function (which expects ff objects and supports parallel processing)
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 2010-04-11 R. Scharpf committed version 1.5.48
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 ** added a few .Rd files
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+2010-04-16 B Carvalho committed version 1.5.49
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+** cosmetics - looking for cause of memory spike
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Browse code

added a few Rd files. Removed metaArray from NAMESPACE

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45865 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/04/2010 16:10:26
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@@ -509,3 +509,9 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
509 509
 ** crlmmIllumina2() and crlmmIlluminaV2() now use the crlmmGT2() 
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 function (which expects ff objects and supports parallel processing)
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 ** updated crlmmIllumina.pdf vignette
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+
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+2010-04-11 R. Scharpf committed version 1.5.48
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+** added a few .Rd files
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+
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+
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+
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45831 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 09/04/2010 07:02:35
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@@ -501,5 +501,11 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
501 501
 ** 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().
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 2010-04-08 B Carvalho committed version 1.5.46
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 ** moved NEWS to inst/
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+2010-04-09 M. Ritchie committed version 1.5.47
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+** fixed bugs in code and removed copy number probes from output 
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+(now saved separately as before - SnpSuperSet not used)
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+** crlmmIllumina2() and crlmmIlluminaV2() now use the crlmmGT2() 
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+function (which expects ff objects and supports parallel processing)
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+** updated crlmmIllumina.pdf vignette
Browse code

NEWS @ inst/

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45815 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/04/2010 11:01:11
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@@ -499,3 +499,7 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
499 499
 
500 500
 2010-04-07 M. Ritchie committed version 1.5.45
501 501
 ** 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().
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+2010-04-08 B Carvalho committed version 1.5.46
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+** moved NEWS to inst/
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45780 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 07/04/2010 06:26:50
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@@ -496,3 +496,6 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
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    with crlmm2
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 ** added crlmmCopynumber2 for parallel support with copy number
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    est. (needs more checking)
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+2010-04-07 M. Ritchie committed version 1.5.45
501
+** 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().
Browse code

added genotype2 and crlmmCopynumber2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45672 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 02/04/2010 03:03:19
Showing1 changed files
... ...
@@ -489,3 +489,10 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
489 489
 
490 490
 ** added parallel/large dataset support to snprma/crlmm
491 491
 ** merged changes on .41 with my local changes
492
+
493
+2010-04-01 R.Scharpf committed version 1.5.44
494
+
495
+** added functions genotype2, cnrma2 for preprocessing and genotyping
496
+   with crlmm2
497
+** added crlmmCopynumber2 for parallel support with copy number
498
+   est. (needs more checking)
Browse code

HPC for snprma/crlmm on Affy

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45498 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 25/03/2010 13:14:54
Showing1 changed files
... ...
@@ -485,3 +485,7 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
485 485
 ** updates to genotype, crlmmIlluminaRS, crlmmCopynumber
486 486
 ** class union of ff_matrix, matrix, and ffdf
487 487
 
488
+2010-03-18 B Carvalho committed version 1.5.42
489
+
490
+** added parallel/large dataset support to snprma/crlmm
491
+** merged changes on .41 with my local changes
Browse code

updates to genotype, crlmmIlluminaRS, and crlmmCopynumber

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45497 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 25/03/2010 13:01:51
Showing1 changed files
... ...
@@ -478,9 +478,10 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
478 478
 ** a few updates to initializeBigMatrix
479 479
 ** show, [ defined for CNSetLM
480 480
 
481
-2010-03-18 R.Scharpf committed version 1.5.38
481
+2010-03-25 R.Scharpf committed version 1.5.41
482 482
 
483 483
 ** import snpCall, snpCallProbability, snpCall<-, snpCallProbability<-
484 484
    from Biobase
485
-** updates to genotype and crlmmIlluminaRS
485
+** updates to genotype, crlmmIlluminaRS, crlmmCopynumber
486 486
 ** class union of ff_matrix, matrix, and ffdf
487
+
Browse code

updated genotype and crlmmIlluminaRS functions. suppressing integer overflow warnings that do not appear to be relevant

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45348 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/03/2010 16:00:25
Showing1 changed files
... ...
@@ -477,3 +477,10 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
477 477
 
478 478
 ** a few updates to initializeBigMatrix
479 479
 ** show, [ defined for CNSetLM
480
+
481
+2010-03-18 R.Scharpf committed version 1.5.38
482
+
483
+** import snpCall, snpCallProbability, snpCall<-, snpCallProbability<-
484
+   from Biobase
485
+** updates to genotype and crlmmIlluminaRS
486
+** class union of ff_matrix, matrix, and ffdf
Browse code

update initializeBigMatrix. methods for CNSetLM

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45324 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 18/03/2010 13:47:33
Showing1 changed files
... ...
@@ -473,3 +473,7 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
473 473
      (currently saving intermediate steps in crlmmIlluminaRS)
474 474
      removed cnOptions function and changed arguments to crlmmCopynumber
475 475
 
476
+2010-03-18 R.Scharpf committed version 1.5.38
477
+
478
+** a few updates to initializeBigMatrix
479
+** show, [ defined for CNSetLM
Browse code

fixed bugs in genotype and crlmmIlluminaRS. changed arguments to crlmmCopynumber. removed cnOptions function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45322 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 18/03/2010 12:19:14
Showing1 changed files
... ...
@@ -467,3 +467,9 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
467 467
 
468 468
 **   added crlmmIlluminaRS to cnrma-functions.R (testing)
469 469
 
470
+2010-03-18 R.Scharpf committed version 1.5.37
471
+
472
+**   fixed bugs in genotype() and crlmmIlluminaRS.
473
+     (currently saving intermediate steps in crlmmIlluminaRS)
474
+     removed cnOptions function and changed arguments to crlmmCopynumber
475
+
Browse code

testing crlmmIlluminaRS in cnrma-functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45221 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/03/2010 01:43:23
Showing1 changed files
... ...
@@ -416,19 +416,29 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
416 416
 
417 417
 2010-03-07 R. Scharpf committed version 1.5.30
418 418
 
419
-- one can use ff in conjunction with affy platforms 5.0 and 6.0
420
-
421
-- more s4-style code
422
-
423
-- 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
424
-
425
-- if ff package is loaded, the assayData elements are ff objects
426
-
427
-- 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.
428
-
429
-- the batchSize argument will run the genotyping (crlmmGT) in batches to reduce the RAM.  The default is batches of size 1000.
430
-
431
-- The crlmm.Rd file contains an example with / without ff for Affymetrix data.
419
+       - one can use ff in conjunction with affy platforms 5.0 and 6.0
420
+       - preprocessing / genotyping is basically the same set of
421
+        commands with either illumina/affy platforms (though
422
+        illumina-users may have to play with some of the options for
423
+        reading idat files
424
+       - if ff package is loaded, the assayData elements are ff objects
425
+
426
+       - the classes all inherit from 'CrlmmContainer' that contains
427
+         an additional slot 'options' and 'genomeAnnotation'.  options
428
+         is a list with the default arguments to snprma, crlmm, etc,
429
+         as well as a few global settings such as 'verbose' and
430
+         'seed'.  I added the genomeAnnotation slot simply because I
431
+         want to be able to use ff-objects for the feature-level data.
432
+         Maybe with setClassUnion we could avoid adding the
433
+         genomeAnnotation slot (and use featureData instead), but I
434
+         didn't have much success with this.
435
+
436
+	 - the batchSize argument will run the genotyping (crlmmGT) in
437
+           batches to reduce the RAM.  The default is batches of size
438
+           1000.
439
+
440
+	 - The crlmm.Rd file contains an example with / without ff
441
+             for Affymetrix data.
432 442
 
433 443
 2010-03-08 M. Ritchie committed version 1.5.31
434 444
  * 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.
436 446
 
437 447
 2010-03-08 R.Scharpf committed version 1.5.32
438 448
 
439
-**	   This is a roll back to version 1.5.24 
449
+**	   Rolled back to version 1.5.24 
440 450
 	   
441 451
 2010-03-08 R.Scharpf committed version 1.5.33
442 452
 
... ...
@@ -447,3 +457,13 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
447 457
 **	  updated DESCRIPTION to import ff
448 458
 **        added AllClasses.R with defitions for ff-derived classes
449 459
 **        temporarily exporting everything in the NAMESPACE
460
+
461
+2010-03-11 R.Scharpf committed version 1.5.35
462
+
463
+**        added genotype() in cnrma-functions -- for preprocessing and
464
+          genotyping affy
465
+
466
+2010-03-14 R.Scharpf committed version 1.5.36
467
+
468
+**   added crlmmIlluminaRS to cnrma-functions.R (testing)
469
+
Browse code

updated description, added AllClasses.R

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45131 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2010 14:53:53
Showing1 changed files
... ...
@@ -441,3 +441,9 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
441 441
 2010-03-08 R.Scharpf committed version 1.5.33
442 442
 
443 443
 **	  Added annotatedDataFrameFrom methods for ff_matrix and ffdf (in utils)
444
+
445
+2010-03-10 R.Scharpf committed version 1.5.34
446
+
447
+**	  updated DESCRIPTION to import ff
448
+**        added AllClasses.R with defitions for ff-derived classes
449
+**        temporarily exporting everything in the NAMESPACE
Browse code

added annotatedDataFrameFrom methods for ff_matrix and ffdf

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45129 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2010 11:45:52
Showing1 changed files
... ...
@@ -438,4 +438,6 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
438 438
 
439 439
 **	   This is a roll back to version 1.5.24 
440 440
 	   
441
+2010-03-08 R.Scharpf committed version 1.5.33
441 442
 
443
+**	  Added annotatedDataFrameFrom methods for ff_matrix and ffdf (in utils)
Browse code

roll back to crlmm version 1.5.24

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45126 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2010 01:27:04
Showing1 changed files
... ...
@@ -433,3 +433,9 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
433 433
 2010-03-08 M. Ritchie committed version 1.5.31
434 434
  * 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()) 
435 435
  * added "humanomni1quadv1b" to validCdfName() in utils.R
436
+
437
+2010-03-08 R.Scharpf committed version 1.5.32
438
+
439
+**	   This is a roll back to version 1.5.24 
440
+	   
441
+

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45084 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 08/03/2010 07:07:43
Showing1 changed files
... ...
@@ -429,3 +429,7 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
429 429
 - the batchSize argument will run the genotyping (crlmmGT) in batches to reduce the RAM.  The default is batches of size 1000.
430 430
 
431 431
 - The crlmm.Rd file contains an example with / without ff for Affymetrix data.
432
+
433
+2010-03-08 M. Ritchie committed version 1.5.31
434
+ * 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()) 
435
+ * added "humanomni1quadv1b" to validCdfName() in utils.R
Browse code

several updates for ff. new classes for affy/illumina processing. More s4-style code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45083 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 08/03/2010 04:46:55
Showing1 changed files
... ...
@@ -413,3 +413,19 @@ then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
413 413
 
414 414
 2010-03-05 M. Ritchie - committed version 1.5.29
415 415
  * crlmmIlluminaV2() now exported.  Added man page crlmmIlluminaV2.Rd
416
+
417
+2010-03-07 R. Scharpf committed version 1.5.30
418
+
419
+- one can use ff in conjunction with affy platforms 5.0 and 6.0
420
+
421
+- more s4-style code
422
+
423
+- 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
424
+
425
+- if ff package is loaded, the assayData elements are ff objects
426
+
427
+- 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.
428
+
429
+- the batchSize argument will run the genotyping (crlmmGT) in batches to reduce the RAM.  The default is batches of size 1000.
430
+
431
+- The crlmm.Rd file contains an example with / without ff for Affymetrix data.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45050 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 05/03/2010 05:23:48
Showing1 changed files
... ...
@@ -410,3 +410,6 @@ Such files arise when scanner settings contain the line <GenerateVersionTwoIdatF
410 410
 If this is modified to <GenerateVersionTwoIdatFiles>true</GenerateVersionTwoIdatFiles>, 
411 411
 then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
412 412
  * Removed AllClasses.R from Collate field in DESCRIPTION file (causes an error in build)
413
+
414
+2010-03-05 M. Ritchie - committed version 1.5.29
415
+ * crlmmIlluminaV2() now exported.  Added man page crlmmIlluminaV2.Rd

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44968 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 02/03/2010 05:33:50
Showing1 changed files
... ...
@@ -386,7 +386,7 @@ is stored in the assayData slot.
386 386
 2010-02-07 B. Carvalho - committed version 1.5.25
387 387
  * Updated requirement of affyio to support Win64
388 388
 
389
-2010-02-20 R. Scharpf - committed version 1.5.25
389
+2010-02-20 R. Scharpf - committed version 1.5.26
390 390
 
391 391
 ** begin adding support for ff
392 392
 
... ...
@@ -400,8 +400,13 @@ is stored in the assayData slot.
400 400
       - B.rda
401 401
       - cn_rmaResult.rda (SKW)
402 402
 
403
-2010-02-21 R. Scharpf - committed version 1.5.26
403
+2010-02-21 R. Scharpf - committed version 1.5.27
404 404
  
405 405
 ** additional support for ff in crlmm and computeCopynumber functions
406 406
 
407
-
407
+2010-03-02 M. Ritchie - committed version 1.5.28
408
+ * Added message to readIDAT() warning that older style IDAT files can not be read in.
409
+Such files arise when scanner settings contain the line <GenerateVersionTwoIdatFiles>false</GenerateVersionTwoIdatFiles>
410
+If this is modified to <GenerateVersionTwoIdatFiles>true</GenerateVersionTwoIdatFiles>, 
411
+then readIDAT() should work. Thanks to Pierre Cherel who reported this error.
412
+ * Removed AllClasses.R from Collate field in DESCRIPTION file (causes an error in build)
Browse code

more ff support

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44783 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 22/02/2010 03:25:51
Showing1 changed files
... ...
@@ -400,4 +400,8 @@ is stored in the assayData slot.
400 400
       - B.rda
401 401
       - cn_rmaResult.rda (SKW)
402 402
 
403
+2010-02-21 R. Scharpf - committed version 1.5.26
404
+ 
405
+** additional support for ff in crlmm and computeCopynumber functions
406
+
403 407
 
Browse code

begin adding support for ff. added an option to use poe

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44778 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 20/02/2010 23:39:45
Showing1 changed files
... ...
@@ -385,3 +385,19 @@ is stored in the assayData slot.
385 385
 
386 386
 2010-02-07 B. Carvalho - committed version 1.5.25
387 387
  * Updated requirement of affyio to support Win64
388
+
389
+2010-02-20 R. Scharpf - committed version 1.5.25
390
+
391
+** begin adding support for ff
392
+
393
+** added use.poe option for nonpolymorphic loci
394
+
395
+** crlmm does not return anything, but saves the following objects:
396
+      - genotypes.rda
397
+      - confs.rda
398
+      - snp_rmaResult.rda  (gns, sns, SNR, SKW, mixtureParams, cdfName)
399
+      - A.rda
400
+      - B.rda
401
+      - cn_rmaResult.rda (SKW)
402
+
403
+
Browse code

Updated requirement of affyio to support Win64

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44545 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/02/2010 15:58:25
Showing1 changed files
... ...
@@ -382,3 +382,6 @@ is stored in the assayData slot.
382 382
 2010-02-05 M. Ritchie - committed version 1.5.24
383 383
  * 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'.
384 384
  * updated the following man pages to reflect the above changes and added in current references:  crlmmIllumina.Rd, crlmm.Rd and readIdatFiles.Rd
385
+
386
+2010-02-07 B. Carvalho - committed version 1.5.25
387
+ * Updated requirement of affyio to support Win64
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44514 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 05/02/2010 03:49:42
Showing1 changed files
... ...
@@ -377,7 +377,8 @@ in the one function to reduce memory usage (not exported as yet)
377 377
 to save memory.  Instead, 'zero', which indicates which SNPs have zero beads 
378 378
 is stored in the assayData slot.
379 379
  * now store 'zero' with copy number AB intensities in preprocessInfinium2()
380
+ * deleted man pages crlmm.Rd and readIdatFiles.Rd added back
380 381
 
381 382
 2010-02-05 M. Ritchie - committed version 1.5.24
382 383
  * 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'.
383
- * updated man page for crlmmIllumina()
384 384
\ No newline at end of file
385
+ * updated the following man pages to reflect the above changes and added in current references:  crlmmIllumina.Rd, crlmm.Rd and readIdatFiles.Rd
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44512 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 05/02/2010 03:27:18
Showing1 changed files
... ...
@@ -377,3 +377,7 @@ in the one function to reduce memory usage (not exported as yet)
377 377
 to save memory.  Instead, 'zero', which indicates which SNPs have zero beads 
378 378
 is stored in the assayData slot.
379 379
  * now store 'zero' with copy number AB intensities in preprocessInfinium2()
380
+
381
+2010-02-05 M. Ritchie - committed version 1.5.24
382
+ * 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'.
383
+ * updated man page for crlmmIllumina()
380 384
\ No newline at end of file
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44484 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 04/02/2010 04:09:27
Showing1 changed files
... ...
@@ -363,9 +363,17 @@ is decoded and scanned
363 363
 
364 364
  * Added 'humanomni1quadv1b" to chip types allowed in RGtoXY()
365 365
 
366
-
367 366
 2010-01-20 R. Scharpf - committed version 1.5.21
368 367
  * Added CopyNumberVariants to DESCRIPTION
369 368
 
370 369
 2010-01-20 R. Scharpf - committed version 1.5.22
371 370
  * restored inst/doc/crlmmDownstream.Rnw
371
+
372
+2010-02-04 M. Ritchie - committed version 1.5.23
373
+ * crlmmIllumina now exported in NAMESPACE (removed at some point)
374
+ * new function crlmmIlluminaV2() which reads in .idats and genotypes 
375
+in the one function to reduce memory usage (not exported as yet)
376
+ * readIdatFiles() modified to no longer store number of beads and beads SE
377
+to save memory.  Instead, 'zero', which indicates which SNPs have zero beads 
378
+is stored in the assayData slot.
379
+ * now store 'zero' with copy number AB intensities in preprocessInfinium2()
Browse code

restored crlmmDownstream.Rnw

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44105 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 20/01/2010 11:20:20
Showing1 changed files
... ...
@@ -366,3 +366,6 @@ is decoded and scanned
366 366
 
367 367
 2010-01-20 R. Scharpf - committed version 1.5.21
368 368
  * Added CopyNumberVariants to DESCRIPTION
369
+
370
+2010-01-20 R. Scharpf - committed version 1.5.22
371
+ * restored inst/doc/crlmmDownstream.Rnw
Browse code

added CopyNumberVariants to DESCRIPTION

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44103 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 20/01/2010 11:15:26
Showing1 changed files
... ...
@@ -362,3 +362,7 @@ is decoded and scanned
362 362
 2009-12-24 M. Ritchie - committed version 1.5.19
363 363
 
364 364
  * Added 'humanomni1quadv1b" to chip types allowed in RGtoXY()
365
+
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+2010-01-20 R. Scharpf - committed version 1.5.21
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+ * Added CopyNumberVariants to DESCRIPTION
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43753 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 24/12/2009 04:06:18
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-* made memory savings to reading and normalization if Illumina data
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+* made memory savings to reading and normalization of Illumina data
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 * Now use 'protocolData' slot to save scan dates instead of saving them in phenoData slot
186 186
 * added vignette for genoytping illumina data (crlmmIllumina.pdf in inst/doc and crlmmIllumina.Rnw in inst/scripts)
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 * Changed stop() to warning() when idats are of different type in readIdatFiles()
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  * moved IRanges and oligoClasses to Depends (DESCRIPTION)
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-2009-12-23 R. Scharpf - commited version 1.5.17
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+2009-12-23 R. Scharpf - committed version 1.5.17
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 ** updated first half of inst/scripts/copynumber.Rnw, as well as a few of the help files
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-2009-12-23 R. Scharpf - commited version 1.5.18
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+2009-12-23 R. Scharpf - committed version 1.5.18
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 ** removed generics for addFeatureAnnotation and GT<-
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+2009-12-24 M. Ritchie - committed version 1.5.19
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+ * Added 'humanomni1quadv1b" to chip types allowed in RGtoXY()
Browse code

removed generics for addFeatureAnnotation and GT<-

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Rob Scharp authored on 23/12/2009 12:55:31
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 ** updated first half of inst/scripts/copynumber.Rnw, as well as a few of the help files
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+
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+2009-12-23 R. Scharpf - commited version 1.5.18
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+
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+** removed generics for addFeatureAnnotation and GT<-
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+
Browse code

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43728 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/12/2009 10:57:10
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  * moved IRanges and oligoClasses to Depends (DESCRIPTION)
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+
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+2009-12-23 R. Scharpf - commited version 1.5.17
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+
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+** updated first half of inst/scripts/copynumber.Rnw, as well as a few of the help files
Browse code

Organizing crlmm for transition with oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43392 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 04/12/2009 18:21:42
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       removed inadvertantly in version 1.3.7, put back]
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  * removed header checking from readIdatFiles() (seems to fail often).  
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       Instead check that the number of SNPs agrees (to within +/- 10K SNPs)
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+2009-12-04 B. Carvalho - committed version 1.5.11
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+
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+ * moved IRanges and oligoClasses to Depends (DESCRIPTION)
Browse code

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unknown authored on 03/12/2009 07:05:16
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  * bug fixed in stripNormalize() [X+16,Y+16 which avoids log(0) = -Inf values, 
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       removed inadvertantly in version 1.3.7, put back]
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+ * removed header checking from readIdatFiles() (seems to fail often).  
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+      Instead check that the number of SNPs agrees (to within +/- 10K SNPs)
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43311 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 01/12/2009 03:07:44
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  * fixed bugs in addFeatureAnnotation.SnpCallSetPlus
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+2009-12-01 M. Ritchie - committed version 1.5.8
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+
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+ * bug fixed in stripNormalize() [X+16,Y+16 which avoids log(0) = -Inf values, 
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+      removed inadvertantly in version 1.3.7, put back]
Browse code

fixed bugs in addFeatureAnnotation.SnpCallSetPlus

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43147 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/11/2009 16:04:12
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  * added CNSet class
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  * segmentData slot in CNSet class is an extension of RangedData (defined in IRanges package)
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-2009-11-19 R. Scharpf - committed version 1.5.6
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+2009-11-19 R. Scharpf - committed version 1.5.6 
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- * fixed bug in initialization of SnpCallSetPlus
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+ * fixed bugs in initialization of SnpCallSetPlus
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+
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+2009-11-19 R. Scharpf - committed version 1.5.7
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+ * fixed bugs in addFeatureAnnotation.SnpCallSetPlus
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Browse code

fixed bug in initialization of SnpCallSetPlus

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Rob Scharp authored on 19/11/2009 15:35:57
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  * added CNSet class
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  * segmentData slot in CNSet class is an extension of RangedData (defined in IRanges package)
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+2009-11-19 R. Scharpf - committed version 1.5.6
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+
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+ * fixed bug in initialization of SnpCallSetPlus
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+
Browse code

cleaned up a few of the classes. defined new class called CNSet to take the place of CrlmmSet

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Rob Scharp authored on 19/11/2009 14:59:04
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  * fixed classes imported from oligoClasses in NAMESPACE
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  * imported 'calls<-' from oligoClasses
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+2009-11-19 R. Scharpf - committed version 1.5.5
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+
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+ * removed a few of the classes (CrlmmSet, CrlmmSetFF, SnpCallSetPlusFF,...)
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+ * added CNSet class
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+ * segmentData slot in CNSet class is an extension of RangedData (defined in IRanges package)
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+
Browse code

Fixes on C code and dependencies on oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43012 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/11/2009 12:54:26
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  - ABset and CrlmmSetList classes are gone. Using SnpCallSetPlus and CrlmmSet
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  - Added class SegmentSet that extends CrlmmSet directly.
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+2009-11-15 B Carvalho - committed version 1.5.4
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+
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+ * removed references to old C code
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+ * added the missing files to the Collate field
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+ * fixed classes imported from oligoClasses in NAMESPACE
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+ * imported 'calls<-' from oligoClasses
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Browse code

numerous changes to the code and class definitions used for copy number estimation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43010 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/11/2009 10:46:23
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  * code cleanup - removed unneeded C code
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+
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+2009-11-15 R. Scharpf - committed version 1.5.3
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+
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+ * numerous changes to the copy number estimation
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+ - ABset and CrlmmSetList classes are gone. Using SnpCallSetPlus and CrlmmSet
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+ - Added class SegmentSet that extends CrlmmSet directly.
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+
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+
Browse code

Removed unneeded C-code and cleaned some crlmm functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@42999 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 14/11/2009 17:26:14
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  * fixed bug in readIdatFiles()
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  * updated crlmmIllumina.Rnw and crlmmIllumina.pdf
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+2009-11-14 B Carvalho - committed version 1.5.2
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+
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+ * code cleanup - removed unneeded C code
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@42633 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 25/10/2009 05:07:25
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  * updated illumina_copynumber vignette
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+2009-10-25 M Ritchie - committed version 1.3.24
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+ * fixed bug in readIdatFiles()
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+ * updated crlmmIllumina.Rnw and crlmmIllumina.pdf
Browse code

updated vignettes for illumina and affy

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@42431 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/10/2009 12:08:21
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 * updated addFeatureAnnotation so that CHR arg not required
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 * fixed bug in nonpolymorphic function -- function checks whether any regions are pseudoautosomal 
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 * fixed bug in list2locusset function (no longer assigns genomewidesnp6 as the default annotation)
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+
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+2009-10-16 R. Scharpf - committed version 1.3.23
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+
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+ * 100*CA, 100*CB are stored in the CA, CB assayDataElements.  The
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+   replacement method automatically converts a matrix on the copy
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+   number scale to an integer representation by scaling by a factor of
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+   100. The accessor methods for CA, CB automatically divide by 100 to
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+   return estimates back on the original copy number scale.
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+
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+ * more debugging of readIdatFiles and illumina copy number vignette.
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+
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+ * updated illumina_copynumber vignette
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+
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+
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+
Browse code

bug fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@42271 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 09/10/2009 12:47:42
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 * 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)
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 * new method: addFeatureAnnotation
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 * support for snp5.0
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+2009-10-04 R. Scharpf - committed version 1.3.22
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+
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+* changed default path argument for readIdatFiles to empty quotes
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+* fixed bug in update method for character strings
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+* updated addFeatureAnnotation so that CHR arg not required
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+* fixed bug in nonpolymorphic function -- function checks whether any regions are pseudoautosomal 
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+* fixed bug in list2locusset function (no longer assigns genomewidesnp6 as the default annotation)
Browse code

changes to crlmmWrapper. updated vignettes in inst/scripts.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@42144 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2009 02:37:32
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 * labeled figures / displayed output of code chunks in the copy number vignette
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 * added bibliography for copy number vignette.  Added file inst/doc/refs.bib
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 * added boxplot method 
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+2009-10-03 R. Scharpf - committed version 1.3.21
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+* modified crlmmWrapper function
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+* modified illumina copy number vignette (still needs debugging)
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+* changed title of copy number vignette
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+* added reference to the crlmm paper
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+* 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)
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+* new method: addFeatureAnnotation
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+* support for snp5.0
Browse code

changes to vignette. removed crlmmIlluminaWrapper function. added boxplot method

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@41178 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 14/08/2009 14:14:25
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 * overhaul of vignette
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 * added update() method for copy number
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 * added documentation and error checks for crlmmWrapper
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+2009-08-14 R. Scharpf - committed version 1.3.19
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+* changes to crlmmWrapper (trying to make this handle the illumina platform as well...still needs testing)
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+  - removed crlmmIlluminaWrapper.Rd, and commented crlmmIlluminaWrapper function
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+* labeled figures / displayed output of code chunks in the copy number vignette
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+* added bibliography for copy number vignette.  Added file inst/doc/refs.bib
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+* added boxplot method 
Browse code

several updates to vignette, documentation, and copy number for illumina.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@41171 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 13/08/2009 19:47:13
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 * changed readIdatFiles function to check whether arrayNames is NULL
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+2009-08-13 R. Scharpf - committed version 1.3.18
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+* move Biobase to Depends
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+* removed GGdata from suggests (problem with loading illuminaHumanv1.db)
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+* overhaul of vignette
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+* added update() method for copy number
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+* added documentation and error checks for crlmmWrapper
Browse code

updated readIdatFiles

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@41017 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/08/2009 15:18:36
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   a) samplesheet5 by get("samplesheet5")
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   b) path by get("path")
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   c) res by get("res")
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+2009-08-04 R. Scharpf - committed version 1.3.17
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+* changed readIdatFiles function to check whether arrayNames is NULL
Browse code

Fixing several warnings and notes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40930 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 31/07/2009 04:51:13
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 * fixed malformed DESCRIPTION file
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+2009-07-31 B Carvalho - committed version 1.3.16
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+* Removed several warnings at the C-level
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+* Fixed several incorrect links in the documentation
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+* Removed multiple notes "no visible binding for global variable"
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+  by replacing, in crlmmIlluminaWrapper and crlmmWrapper,
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+  a) samplesheet5 by get("samplesheet5")
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+  b) path by get("path")
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+  c) res by get("res")
Browse code

Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40809 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 24/07/2009 03:16:33
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 * made memory savings to reading and normalization if Illumina data
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-* Now use 'scanDates' slot to save scan dates instead of saving them in phenoData slot
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+* Now use 'protocolData' slot to save scan dates instead of saving them in phenoData slot
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 * added vignette for genoytping illumina data (crlmmIllumina.pdf in inst/doc and crlmmIllumina.Rnw in inst/scripts)
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 * Changed stop() to warning() when idats are of different type in readIdatFiles()
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-* scanDates replacement method for CrlmmSetList objects
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+* protocolData replacement method for CrlmmSetList objects
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 * added .man page for .computeCopynumber 
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Browse code

fixed malformed DESCRIPTION file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40652 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/07/2009 16:13:38
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 * fixed bug 'DF.PRIOR not found'
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+2009-07-16 R Scharpf - committed version 1.3.14
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+* fixed malformed DESCRIPTION file
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Browse code

fixed bug in DF.PRIOR not found

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40651 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/07/2009 16:08:27
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 * added .man page for .computeCopynumber 
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-* Suggests VanillaICE (>= 1.7.8)  -- needed to run the copynumber.Rnw vignette
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+* Suggests VanillaICE (>= 1.7.8)  -- needed to run the copynumber.Rnw
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+  vignette
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+2009-07-16 R Scharpf - committed version 1.3.13
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+
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+* fixed bug 'DF.PRIOR not found'
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Browse code

added scanDates<- for CrlmmSetList. Suggests VanillaICE>=1.7.8

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Rob Scharp authored on 16/07/2009 13:32:48
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 * computeCopynumber requires 10 or more samples
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+2009-07-16 R Scharpf - committed version 1.3.12
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+* scanDates replacement method for CrlmmSetList objects
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+* added .man page for .computeCopynumber 
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+* Suggests VanillaICE (>= 1.7.8)  -- needed to run the copynumber.Rnw vignette
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+
Browse code

computeCopynumber requires 10 or more samples

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40620 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 14/07/2009 19:45:10
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   - copy number parameters in the featureData of the CopyNumberSet
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     element are thresholded
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+2009-07-14 R Scharpf - committed version 1.3.11
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+* computeCopynumber requires 10 or more samples
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Browse code

computeCopynumber returns CrlmmSetList object

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40618 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 14/07/2009 17:22:19
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 * fixed bugs in biasAdj and biasAdjNP
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+2009-07-09 R Scharpf - committed version 1.3.10
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+* changed defaults for crlmmWrapper: save.it=FALSE
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+* splitByChr method looks for 'chr' or 'chromosome' in colnames 
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+* sample-specific standard deviations in the .getEmission function
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+* add check for duplicated positions in creating locusset object
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+* computeCopynumber returns an object of class CrlmmSetList
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+  
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+  - dimnames for the elements in the list are the same
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+  - elements in the list are ordered by chromosome and physical
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+    position
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+  - copy number parameters in the featureData of the CopyNumberSet
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+    element are thresholded
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+
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+
Browse code

fixed bugs in bias adjustment functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40544 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 07/07/2009 20:07:44
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 * some improvements to chromosome X copy number estimation
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+2009-07-06 R Scharpf - committed version 1.3.9
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+* fixed bugs in biasAdj and biasAdjNP
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+
Browse code

beginning of copy number methods for illumina. some work on copy number estimation for chromosome X

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40527 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 06/07/2009 19:24:27
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 * added vignette for genoytping illumina data (crlmmIllumina.pdf in inst/doc and crlmmIllumina.Rnw in inst/scripts)
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 * Changed stop() to warning() when idats are of different type in readIdatFiles()
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Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40465 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 02/07/2009 07:39:23
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 * updated computeCopynumber
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 * export A, B methods for ABset class
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+* made memory savings to reading and normalization if Illumina data
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+* Now use 'scanDates' slot to save scan dates instead of saving them in phenoData slot
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+* added vignette for genoytping illumina data (crlmmIllumina.pdf in inst/doc and crlmmIllumina.Rnw in inst/scripts)
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+* Changed stop() to warning() when idats are of different type in readIdatFiles()
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Browse code

update computeCopynumber, added .R files for new classes/methods

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40371 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 29/06/2009 12:29:11
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Browse code

added classes/methods for intermediate files and copy number analysis; added wrapper for preprocessing and genotypes.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40309 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 25/06/2009 12:54:08
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+* created CrlmmSetList, ABset, and CopyNumberSet classes.  
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+* crlmmWrapper does normalization / genotyping and optionally splits
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updated biasAdjNP and biasAdj functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40036 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 09/06/2009 14:23:02
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+* fixed bug in the biasAdjNP function.  updated biasAdj function
Browse code

Adding batchQC to phenoData

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@39998 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/06/2009 14:49:43
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Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@39329 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 07/05/2009 00:11:16
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fixed bug in nonpolymorphic function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@39171 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 27/04/2009 14:11:59
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+* Fixed bug in nonpolymorphic() function
Browse code

added copy number vignette for illumina. see inst/scripts

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38665 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 09/04/2009 18:09:04
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 * Fixed downstream vignette to account for the SnpSet object being returned by crlmm
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 * Fixed some minor status messages
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Browse code

Fixed some status messages and downstream vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38586 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 08/04/2009 03:15:55
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Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38585 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 08/04/2009 02:01:07
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 * Removed 'svn:executable' property of readIdatFiles.Rd
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change to internal function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38584 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 08/04/2009 00:58:49
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fix bug in cnrma. cnrma now accepts other cdfNames

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38580 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 07/04/2009 23:32:21
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fixed bug in cnrma

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38566 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 07/04/2009 19:57:07
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updated copy number estimation for chromosome X

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38549 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 07/04/2009 13:12:50
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Added documentation for SNPRMA

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38548 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/04/2009 11:22:53
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added cdfName argument to computeCopynumber

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38546 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 07/04/2009 10:01:06
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   - fix a few bugs
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Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38494 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 06/04/2009 05:19:27
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 * simplified some of the preliminary steps for the computeCopynumber function
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 * added function to extract the date from the celfile headers (celDates)
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+is decoded and scanned
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+* results from crlmmIllumina() now saved as 'SnpSet' just like crlmm()
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+* reorganised Illumina preprocessing functions slightly to
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+  - allow copy number intensities to be saved along with snp intensities
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+  - make use of new indexing objects in the chip specific crlmm data packages
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+  - fix a few bugs
Browse code

fixed location/scale for chromosome X in oneBatch function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38486 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/04/2009 20:10:07
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Browse code

Updated TODO/DESCRIPTION

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38475 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/04/2009 20:07:11
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Browse code

added a few items to the TODOs

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38459 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 03/04/2009 09:37:26
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added normalize.quantiles to importFrom() field in NAMESPACE and updated man pages

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38364 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 01/04/2009 06:24:30
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Browse code

added code to handle illumina snp array data

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38297 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 30/03/2009 02:25:09
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Browse code

updated cnrma function and the copy number vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38290 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 29/03/2009 19:59:40
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Browse code

Incorporating changes recommended by reviewer

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38278 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 28/03/2009 18:14:19
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Browse code

Modified warning message to give one reason recalibration may not happen

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Benilton Carvalho authored on 28/03/2009 15:08:16
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Browse code

crlmm returns a SnpSet object

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38275 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 28/03/2009 04:43:33
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updated copynumber vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38184 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 25/03/2009 13:27:44
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Browse code

changes to computeCopynumber function. Exporting wrapper for extracting dates from the cel file header

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Rob Scharp authored on 25/03/2009 13:12:49
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