1. crlmm
  2. TODO
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
Showing 1 changed files
TODO
History View file @ d3bb3c5
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ 5fcfed7
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ a13f66d
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ bfabb22
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ 824cfde
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ 2ae7850
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ b9c7172
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ 45dab54
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ 38fb1b8
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ b5bb7de
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ cd3930b
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ e446e21
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ 95d22b5
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ f8af2ff
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ c027cd7
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ f32a09d
... ... 
@@ -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
Showing 1 changed files
TODO
History View file @ 3620e6b
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 
+#####################################