Browse code

updating todo

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50818 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 11/11/2010 12:22:25
Showing1 changed files
... ...
@@ -23,6 +23,8 @@ B Carvalho
23 23
 
24 24
 - crlmm should return results in CHP files
25 25
 
26
+- crlmm2() with save.it=TRUE must save the original preprocessed intensities
27
+
26 28
   ***********************************************************
27 29
   *                                                         *       
28 30
   *                FOR CNRMA                                *
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
... ...
@@ -9,47 +9,53 @@ Depends just to get rid of annoying warnings while transitioning.
9 9
 - Allele plots
10 10
 - M v S plots
11 11
 
12
-R. Scharpf 
13
- 
14
- - harmonize CNSet and FFSet classes
15
-   use-cases:
16
-      - import S3 classes and methods from ff in the NAMESPACE (but this would require installing ff)
17
-
18
-      - initialization of FFSet  (can it extend CNSet directly?)
19
-      - subsetting of FFSet objects
20
-      - snp-specific plots  (FFSet or CNSet)
21
-      - batch effect plots  (FFSet or CNSet)
22
-      - with cbs
23
-      - with hmm
24
- - ff support for Illumina platforms
25
- - fix all the install warnings
26
- - add README file to inst/scripts to outline the vignettes
27
-   Vignettes:
28
-      copynumber_SmallData.Rnw    (Affy 5.0 or Affy 6.0.  Fewer than 300 samples)
29
-      copynumber_BigData.Rnw      (Affy 5.0 or Affy 6.0.  300+ samples.  Requires ff package.)
30
-      illumina_copynumber_small.Rnw  (Illumina platforms.  Fewer than 300 samples)
31
-      illumina_copynumber_big.Rnw    (Illumina platforms.  More than 300 samples.  Requires ff package.)
32
- - documentation for FFSet class/methods
33
- - bias adjustment for X chromosome
34
- - where to find examples downstream (smoothing)
35
- - downstream objects should be similar whether using ff or regular matrices
36
-
37
-## this should be moved to vanillaice
38
-## - Allow a copy-neutral ROH state by not having an equal prior on the
39
-##    ellipses.  For instance,
40
-##
41
-##     normal state:  1/4 AA, 1/2 AB, 1/4 BB
42
-##    
43
-##    copy-neutral ROH:  (1-epsilon)/2 AA,  epsilon AB,  (1-epsilon)/2
44
-##    BB
12
+R. Scharpf (after next release)
13
+
14
+- crlmm should return a SnpSet object with elements A, B, calls, and
15
+  confs in the assayData when save.it=TRUE.  These objects can be very
16
+  big, so...  
17
+
18
+- crlmm function should have an option to return nothing and write to
19
+  file a SnpSet object for each chromosome.  This would help the copy
20
+  number part that runs by chromosome
45 21
 
46 22
 B Carvalho
47 23
 
48
-- crlmm should return results in CHP files (still can't write CHP files)
49
-- add parallel support (normalization and summarization)
24
+- crlmm should return results in CHP files
25
+
26
+  ***********************************************************
27
+  *                                                         *       
28
+  *                FOR CNRMA                                *
29
+  *                                                         *
30
+  ***********************************************************
31
+
32
+  o Bias adjustment for X chromosome
33
+
34
+  o Adjust nu for altered copy number (crosshyb)
35
+
36
+  o Should store parameters in something besides the featureData slot
37
+
38
+    - Perhaps add a matrix slot for parameters and a slot for batch.
39
+
40
+    - Need accessors
41
+
42
+    - how to store parameters for chromosome X (should be nu_A_male,
43
+      nu_A_female, etc.)?
44
+
45
+  o Provide a SNP- and sample-specific estimate of the variance for
46
+    computing emission probabilities.  (Currently, only SNP-specific)
47
+
48
+    (DONE -- version 1.3.10
50 49
 
50
+  o Allow a copy-neutral ROH state by not having an equal prior on the
51
+    ellipses.  For instance,
51 52
 
53
+    normal state:  1/4 AA, 1/2 AB, 1/4 BB
54
+    
55
+    copy-neutral ROH:  (1-epsilon)/2 AA,  epsilon AB,  (1-epsilon)/2
56
+    BB
52 57
 
58
+  o Define a class that contains settings for genotyping/copynumber estimation
53 59
 
54 60
 
55 61
 
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
... ...
@@ -9,54 +9,47 @@ Depends just to get rid of annoying warnings while transitioning.
9 9
 - Allele plots
10 10
 - M v S plots
11 11
 
12
-R. Scharpf (after next release)
13
-
14
-- crlmm should return a SnpSet object with elements A, B, calls, and
15
-  confs in the assayData when save.it=TRUE.  These objects can be very
16
-  big, so...  
17
-
18
-- crlmm function should have an option to return nothing and write to
19
-  file a SnpSet object for each chromosome.  This would help the copy
20
-  number part that runs by chromosome
12
+R. Scharpf 
13
+ 
14
+ - harmonize CNSet and FFSet classes
15
+   use-cases:
16
+      - import S3 classes and methods from ff in the NAMESPACE (but this would require installing ff)
17
+
18
+      - initialization of FFSet  (can it extend CNSet directly?)
19
+      - subsetting of FFSet objects
20
+      - snp-specific plots  (FFSet or CNSet)
21
+      - batch effect plots  (FFSet or CNSet)
22
+      - with cbs
23
+      - with hmm
24
+ - ff support for Illumina platforms
25
+ - fix all the install warnings
26
+ - add README file to inst/scripts to outline the vignettes
27
+   Vignettes:
28
+      copynumber_SmallData.Rnw    (Affy 5.0 or Affy 6.0.  Fewer than 300 samples)
29
+      copynumber_BigData.Rnw      (Affy 5.0 or Affy 6.0.  300+ samples.  Requires ff package.)
30
+      illumina_copynumber_small.Rnw  (Illumina platforms.  Fewer than 300 samples)
31
+      illumina_copynumber_big.Rnw    (Illumina platforms.  More than 300 samples.  Requires ff package.)
32
+ - documentation for FFSet class/methods
33
+ - bias adjustment for X chromosome
34
+ - where to find examples downstream (smoothing)
35
+ - downstream objects should be similar whether using ff or regular matrices
36
+
37
+## this should be moved to vanillaice
38
+## - Allow a copy-neutral ROH state by not having an equal prior on the
39
+##    ellipses.  For instance,
40
+##
41
+##     normal state:  1/4 AA, 1/2 AB, 1/4 BB
42
+##    
43
+##    copy-neutral ROH:  (1-epsilon)/2 AA,  epsilon AB,  (1-epsilon)/2
44
+##    BB
21 45
 
22 46
 B Carvalho
23 47
 
24 48
 - crlmm should return results in CHP files (still can't write CHP files)
25 49
 - add parallel support (normalization and summarization)
26 50
 
27
-  ***********************************************************
28
-  *                                                         *       
29
-  *                FOR CNRMA                                *
30
-  *                                                         *
31
-  ***********************************************************
32
-
33
-  o Bias adjustment for X chromosome
34
-
35
-  o Adjust nu for altered copy number (crosshyb)
36
-
37
-  o Should store parameters in something besides the featureData slot
38
-
39
-    - Perhaps add a matrix slot for parameters and a slot for batch.
40
-
41
-    - Need accessors
42
-
43
-    - how to store parameters for chromosome X (should be nu_A_male,
44
-      nu_A_female, etc.)?
45
-
46
-  o Provide a SNP- and sample-specific estimate of the variance for
47
-    computing emission probabilities.  (Currently, only SNP-specific)
48
-
49
-    (DONE -- version 1.3.10
50
-
51
-  o Allow a copy-neutral ROH state by not having an equal prior on the
52
-    ellipses.  For instance,
53 51
 
54
-    normal state:  1/4 AA, 1/2 AB, 1/4 BB
55
-    
56
-    copy-neutral ROH:  (1-epsilon)/2 AA,  epsilon AB,  (1-epsilon)/2
57
-    BB
58 52
 
59
-  o Define a class that contains settings for genotyping/copynumber estimation
60 53
 
61 54
 
62 55
 
Browse code

Updated contact info and TODO

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@44787 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 22/02/2010 13:25:02
Showing1 changed files
... ...
@@ -21,7 +21,8 @@ R. Scharpf (after next release)
21 21
 
22 22
 B Carvalho
23 23
 
24
-- crlmm should return results in CHP files
24
+- crlmm should return results in CHP files (still can't write CHP files)
25
+- add parallel support (normalization and summarization)
25 26
 
26 27
   ***********************************************************
27 28
   *                                                         *       
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
Showing1 changed files
... ...
@@ -1,3 +1,7 @@
1
+## IMPORTANT 
2
+- move IRanges and oligoClasses back to Suggests? BC moved them to
3
+Depends just to get rid of annoying warnings while transitioning.
4
+
1 5
 #####################################
2 6
 ### FOR CRLMM
3 7
 #####################################
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
Showing1 changed files
... ...
@@ -51,7 +51,7 @@ B Carvalho
51 51
     copy-neutral ROH:  (1-epsilon)/2 AA,  epsilon AB,  (1-epsilon)/2
52 52
     BB
53 53
 
54
-  o add caConfidence and cbConfidence slots (but what about the correlation)
54
+  o Define a class that contains settings for genotyping/copynumber estimation
55 55
 
56 56
 
57 57
 
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
Showing1 changed files
... ...
@@ -35,5 +35,27 @@ B Carvalho
35 35
 
36 36
     - Need accessors
37 37
 
38
+    - how to store parameters for chromosome X (should be nu_A_male,
39
+      nu_A_female, etc.)?
40
+
41
+  o Provide a SNP- and sample-specific estimate of the variance for
42
+    computing emission probabilities.  (Currently, only SNP-specific)
43
+
44
+    (DONE -- version 1.3.10
45
+
46
+  o Allow a copy-neutral ROH state by not having an equal prior on the
47
+    ellipses.  For instance,
48
+
49
+    normal state:  1/4 AA, 1/2 AB, 1/4 BB
50
+    
51
+    copy-neutral ROH:  (1-epsilon)/2 AA,  epsilon AB,  (1-epsilon)/2
52
+    BB
53
+
54
+  o add caConfidence and cbConfidence slots (but what about the correlation)
55
+
56
+
57
+
58
+
59
+
38 60
 
39 61
 
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
Showing1 changed files
... ...
@@ -19,16 +19,21 @@ B Carvalho
19 19
 
20 20
 - crlmm should return results in CHP files
21 21
 
22
-#####################################
23
-### FOR CNRMA
24
-#####################################
25
-- Bias adjustment for X chromosome
22
+  ***********************************************************
23
+  *                                                         *       
24
+  *                FOR CNRMA                                *
25
+  *                                                         *
26
+  ***********************************************************
27
+
28
+  o Bias adjustment for X chromosome
29
+
30
+  o Adjust nu for altered copy number (crosshyb)
26 31
 
27
-- adjust nu for altered copy number (crosshyb)
32
+  o Should store parameters in something besides the featureData slot
28 33
 
29
-- should store parameters in something besides the featureData slot
34
+    - Perhaps add a matrix slot for parameters and a slot for batch.
30 35
 
31
-        - Perhaps add a slot for parameters and a slot for batch.
36
+    - Need accessors
32 37
 
33 38
 
34 39
 
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
Showing1 changed files
... ...
@@ -23,9 +23,12 @@ B Carvalho
23 23
 ### FOR CNRMA
24 24
 #####################################
25 25
 - Bias adjustment for X chromosome
26
+
26 27
 - adjust nu for altered copy number (crosshyb)
27
-- a class for the assay data elements and metadata -- oligoSnpSet?
28
-      - should we consider a name change -- e.g., LocusSet
29
-- a class for the intermediate files and methods for SNP-specific plots
30
-- uncertainty estimates for copy number.  Put in cnConfidence slot
28
+
29
+- should store parameters in something besides the featureData slot
30
+
31
+        - Perhaps add a slot for parameters and a slot for batch.
32
+
33
+
31 34
 
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
Showing1 changed files
... ...
@@ -1,7 +1,6 @@
1 1
 #####################################
2 2
 ### FOR CRLMM
3 3
 #####################################
4
-- Fix downstream vignette
5 4
 - Add RS ids to annotation packages
6 5
 - Allele plots
7 6
 - M v S plots
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
Showing1 changed files
... ...
@@ -16,6 +16,10 @@ R. Scharpf (after next release)
16 16
   file a SnpSet object for each chromosome.  This would help the copy
17 17
   number part that runs by chromosome
18 18
 
19
+B Carvalho
20
+
21
+- crlmm should return results in CHP files
22
+
19 23
 #####################################
20 24
 ### FOR CNRMA
21 25
 #####################################
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
Showing1 changed files
... ...
@@ -6,6 +6,15 @@
6 6
 - Allele plots
7 7
 - M v S plots
8 8
 
9
+R. Scharpf (after next release)
10
+
11
+- crlmm should return a SnpSet object with elements A, B, calls, and
12
+  confs in the assayData when save.it=TRUE.  These objects can be very
13
+  big, so...  
14
+
15
+- crlmm function should have an option to return nothing and write to
16
+  file a SnpSet object for each chromosome.  This would help the copy
17
+  number part that runs by chromosome
9 18
 
10 19
 #####################################
11 20
 ### FOR CNRMA
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
Showing1 changed files
... ...
@@ -1,7 +1,7 @@
1 1
 #####################################
2 2
 ### FOR CRLMM
3 3
 #####################################
4
-- Decide on output format (BC vote: eSet-like)
4
+- Fix downstream vignette
5 5
 - Add RS ids to annotation packages
6 6
 - Allele plots
7 7
 - M v S plots
Browse code

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38183 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 25/03/2009 13:12:49
Showing1 changed files
... ...
@@ -10,6 +10,10 @@
10 10
 #####################################
11 11
 ### FOR CNRMA
12 12
 #####################################
13
-- Rob, can you run a: 'grep ROB *' under R/? There are
14
-  some notes for you there. Basically because I changed
15
-  a few things that I'm not so sure of.
13
+- Bias adjustment for X chromosome
14
+- adjust nu for altered copy number (crosshyb)
15
+- a class for the assay data elements and metadata -- oligoSnpSet?
16
+      - should we consider a name change -- e.g., LocusSet
17
+- a class for the intermediate files and methods for SNP-specific plots
18
+- uncertainty estimates for copy number.  Put in cnConfidence slot
19
+
Browse code

Fixed notes on 'no visible bindings'

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@37951 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 14/03/2009 15:03:05
Showing1 changed files
... ...
@@ -2,7 +2,6 @@
2 2
 ### FOR CRLMM
3 3
 #####################################
4 4
 - Decide on output format (BC vote: eSet-like)
5
-- Helper to convert to snpMatrix
6 5
 - Add RS ids to annotation packages
7 6
 - Allele plots
8 7
 - M v S plots
... ...
@@ -11,19 +10,6 @@
11 10
 #####################################
12 11
 ### FOR CNRMA
13 12
 #####################################
14
-- fix the following 2 items
15
-* checking R code for possible problems ... NOTE
16
-cnrma: no visible global function definition for ‘getCnvFid’
17
-cnrma: no visible binding for global variable ‘reference’
18
-coefs: no visible binding for global variable ‘nu’
19
-coefs: no visible binding for global variable ‘phi’
20
-coefs: no visible binding for global variable ‘nu.se’
21
-coefs: no visible binding for global variable ‘phi.se’
22
-
23
-* checking for unstated dependencies in R code ... WARNING
24
-'library' or 'require' calls not declared from:
25
-  affyio splines Biobase genefilter
26
-
27
-* checking for missing documentation entries ... WARNING
28
-Undocumented code objects:
29
-  computeCnBatch
13
+- Rob, can you run a: 'grep ROB *' under R/? There are
14
+  some notes for you there. Basically because I changed
15
+  a few things that I'm not so sure of.
Browse code

Added solution for vignettes that depend on external data. Fixed documentation. Added CHANGES and TODO files.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@37677 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/03/2009 22:34:22
Showing1 changed files
... ...
@@ -3,11 +3,27 @@
3 3
 #####################################
4 4
 - Decide on output format (BC vote: eSet-like)
5 5
 - Helper to convert to snpMatrix
6
-- Vignette with non-trivial use of crlmm (use Vince's)
7
-- Add RS ids
6
+- Add RS ids to annotation packages
8 7
 - Allele plots
9 8
 - M v S plots
10 9
 
10
+
11 11
 #####################################
12 12
 ### FOR CNRMA
13 13
 #####################################
14
+- fix the following 2 items
15
+* checking R code for possible problems ... NOTE
16
+cnrma: no visible global function definition for ‘getCnvFid’
17
+cnrma: no visible binding for global variable ‘reference’
18
+coefs: no visible binding for global variable ‘nu’
19
+coefs: no visible binding for global variable ‘phi’
20
+coefs: no visible binding for global variable ‘nu.se’
21
+coefs: no visible binding for global variable ‘phi.se’
22
+
23
+* checking for unstated dependencies in R code ... WARNING
24
+'library' or 'require' calls not declared from:
25
+  affyio splines Biobase genefilter
26
+
27
+* checking for missing documentation entries ... WARNING
28
+Undocumented code objects:
29
+  computeCnBatch
Browse code

Improving package organization

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@37668 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 02/03/2009 14:22:41
Showing1 changed files
1 1
new file mode 100644
... ...
@@ -0,0 +1,13 @@
1
+#####################################
2
+### FOR CRLMM
3
+#####################################
4
+- Decide on output format (BC vote: eSet-like)
5
+- Helper to convert to snpMatrix
6
+- Vignette with non-trivial use of crlmm (use Vince's)
7
+- Add RS ids
8
+- Allele plots
9
+- M v S plots
10
+
11
+#####################################
12
+### FOR CNRMA
13
+#####################################