1. crlmm
  2. R
  3. AllGenerics.R
Browse code

merge local changes with dan's changes on bioc

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@72708 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 20/01/2013 18:31:47
Showing 1 changed files
R/AllGenerics.R
History View file @ 3ad9a18
... ... 
@@ -105,3 +105,7 @@ setGeneric("predictionRegion", function(object, copyNumber=0:4)
105 105 
 setGeneric("xyplot", useAsDefault=function(x, data, ...) lattice::xyplot(x, data,...))
106 106 
 setGeneric("xyplotcrlmm", function(x, data, predictRegion,...) standardGeneric("xyplotcrlmm"))
107 107 
 setGeneric("calculateRBaf", function(object, batch.name, chrom) standardGeneric("calculateRBaf"))
108 
+
109 
+##setGeneric("mixtureParams<-", function(object,value) standardGeneric("mixtureParams<-"))
110 
+setGeneric("OligoSetList", function(object,...) standardGeneric("OligoSetList"))
111 
+setGeneric("BafLrrSetList", function(object,...) standardGeneric("BafLrrSetList"))
Browse code

Merge branch 'collab'

* collab: (34 commits)
revert change to IlluminaPreprocessCN
fix bug in isValidCdfName
print warning when all features in a batch of probes are flagged, but allow processing to continue
add utility cleancdfnames
Add validCdfNames.Rd
export validCdfNames
imputeGender fix when chromosome Y not available
Use splitIndicesByLength(index, ocSamples/getDoParWorkers())
Can not allocate vector of size XG with genotype.Illumina. Use splitIndicesByNode() only if the length of the list is greater than the split from splitIndicesByLength(). Otherwise, split by length using ocSamples()
update .gitignore
Add make.unique for sampleSheet$Sample_ID in readIdatFiles
bug in description
ensure sample ids stored in samplesheet are unique when constructing cnSet object
update oligoClasses dependency
update unit test for genotype.Illumina
revert change in constructInf call from genotype.Illumina
Update genotype.Rd
edit ACN function
1.15.6 use make.unique(basename(arrayNames)) to allow processing of Illumina samples with duplicated barcodes
check that sample identifies are unique in crlmm function
...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@67435 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 08/07/2012 19:00:03
Showing 1 changed files
R/AllGenerics.R
History View file @ 063b3d1
... ... 
@@ -104,4 +104,4 @@ setGeneric("predictionRegion", function(object, copyNumber=0:4)
104 104 
 	   standardGeneric("predictionRegion"))
105 105 
 setGeneric("xyplot", useAsDefault=function(x, data, ...) lattice::xyplot(x, data,...))
106 106 
 setGeneric("xyplotcrlmm", function(x, data, predictRegion,...) standardGeneric("xyplotcrlmm"))
107 
-setGeneric("calculateRBaf", function(object, batch.name) standardGeneric("calculateRBaf"))
107 
+setGeneric("calculateRBaf", function(object, batch.name, chrom) standardGeneric("calculateRBaf"))
Browse code

Add calculateRBaf method

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58666 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:50:37
Showing 1 changed files
R/AllGenerics.R
History View file @ 4c4e930
... ... 
@@ -104,3 +104,4 @@ setGeneric("predictionRegion", function(object, copyNumber=0:4)
104 104 
 	   standardGeneric("predictionRegion"))
105 105 
 setGeneric("xyplot", useAsDefault=function(x, data, ...) lattice::xyplot(x, data,...))
106 106 
 setGeneric("xyplotcrlmm", function(x, data, predictRegion,...) standardGeneric("xyplotcrlmm"))
107 
+setGeneric("calculateRBaf", function(object, batch.name) standardGeneric("calculateRBaf"))
Browse code

Remove snpNames method and generic

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58665 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:50:30
Showing 1 changed files
R/AllGenerics.R
History View file @ 7818b53
... ... 
@@ -5,7 +5,7 @@ setGeneric("cnNames", function(object) standardGeneric("cnNames"))
5 5 
 ##setGeneric("computeCopynumber", function(object, ...) standardGeneric("computeCopynumber"))
6 6 
 ##setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
7 7 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
8 
-setGeneric("snpNames", function(object) standardGeneric("snpNames"))
8 
+##setGeneric("snpNames", function(object) standardGeneric("snpNames"))
9 9
10 10 
 setGeneric("CA", function(object, ...) standardGeneric("CA"))
11 11 
 setGeneric("CB", function(object, ...) standardGeneric("CB"))
Browse code

Update generics for posteriorProbability and calculatePosteriorMean (exclude weight from generic of calculatePosteriorMean)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58637 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:47:35
Showing 1 changed files
R/AllGenerics.R
History View file @ 96fb65c
... ... 
@@ -95,9 +95,9 @@ setGeneric("flags<-", function(object, value) standardGeneric("flags<-"))
95 95 
 setGeneric("posteriorMean", function(object) standardGeneric("posteriorMean"))
96 96 
 setGeneric("posteriorMean<-", function(object, value) standardGeneric("posteriorMean<-"))
97 97
98 
-setGeneric("posteriorProbability", function(object, predictRegion, copyNumber=0:4)
98 
+setGeneric("posteriorProbability", function(object, predictRegion, copyNumber=0:4, w)
99 99 
 	   standardGeneric("posteriorProbability"))
100 
-setGeneric("calculatePosteriorMean", function(object, posteriorProb, copyNumber=0:4, w, ...)
100 
+setGeneric("calculatePosteriorMean", function(object, posteriorProb, copyNumber=0:4, ...)
101 101 
 	   standardGeneric("calculatePosteriorMean"))
102 102
103 103 
 setGeneric("predictionRegion", function(object, copyNumber=0:4)
Browse code

Update predictionRegion to return arrays in the mu and cov list elements (prediction regions are batch-specific)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58635 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:47:24
Showing 1 changed files
R/AllGenerics.R
History View file @ 0a5dbc0
... ... 
@@ -102,3 +102,5 @@ setGeneric("calculatePosteriorMean", function(object, posteriorProb, copyNumber=
102 102
103 103 
 setGeneric("predictionRegion", function(object, copyNumber=0:4)
104 104 
 	   standardGeneric("predictionRegion"))
105 
+setGeneric("xyplot", useAsDefault=function(x, data, ...) lattice::xyplot(x, data,...))
106 
+setGeneric("xyplotcrlmm", function(x, data, predictRegion,...) standardGeneric("xyplotcrlmm"))
Browse code

Add generics and methods for predictionRegion, posteriorProbability, and calculatePosteriorMean.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58630 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:46:51
Showing 1 changed files
R/AllGenerics.R
History View file @ e516fad
... ... 
@@ -95,5 +95,10 @@ setGeneric("flags<-", function(object, value) standardGeneric("flags<-"))
95 95 
 setGeneric("posteriorMean", function(object) standardGeneric("posteriorMean"))
96 96 
 setGeneric("posteriorMean<-", function(object, value) standardGeneric("posteriorMean<-"))
97 97
98 
+setGeneric("posteriorProbability", function(object, predictRegion, copyNumber=0:4)
99 
+	   standardGeneric("posteriorProbability"))
100 
+setGeneric("calculatePosteriorMean", function(object, posteriorProb, copyNumber=0:4, w, ...)
101 
+	   standardGeneric("calculatePosteriorMean"))
98 102
99 
-
103 
+setGeneric("predictionRegion", function(object, copyNumber=0:4)
104 
+	   standardGeneric("predictionRegion"))
Browse code

fixed cyclic namespace dependency by updating version dependencies in DESCRIPTION, and updating other bioc packages

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53341 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 02/03/2011 00:59:03
Showing 1 changed files
R/AllGenerics.R
History View file @ c75c54c
... ... 
@@ -92,5 +92,8 @@ setGeneric("tau2A<-", function(object, value) standardGeneric("tau2A<-"))
92 92 
 setGeneric("tau2B<-", function(object, value) standardGeneric("tau2B<-"))
93 93 
 setGeneric("flags<-", function(object, value) standardGeneric("flags<-"))
94 94
95 
+setGeneric("posteriorMean", function(object) standardGeneric("posteriorMean"))
96 
+setGeneric("posteriorMean<-", function(object, value) standardGeneric("posteriorMean<-"))
97 
+
95 98
96 99
Browse code

removed generics and methods for sigma2A and sigma2B

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49141 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:41:06
Showing 1 changed files
R/AllGenerics.R
History View file @ a521b1a
... ... 
@@ -57,16 +57,12 @@ setGeneric("madB.AB<-", function(object, value) standardGeneric("madB.AB<-"))
57 57 
 setGeneric("madB.BB<-", function(object, value) standardGeneric("madB.BB<-"))
58 58
59 59 
 setGeneric("tau2A.AA", function(object) standardGeneric("tau2A.AA"))
60 
-##setGeneric("tau2A.AB", function(object) standardGeneric("tau2A.AB"))
61 60 
 setGeneric("tau2A.BB", function(object) standardGeneric("tau2A.BB"))
62 61 
 setGeneric("tau2B.AA", function(object) standardGeneric("tau2B.AA"))
63 
-##setGeneric("tau2B.AB", function(object) standardGeneric("tau2B.AB"))
64 62 
 setGeneric("tau2B.BB", function(object) standardGeneric("tau2B.BB"))
65 63 
 setGeneric("tau2A.AA<-", function(object, value) standardGeneric("tau2A.AA<-"))
66 
-##setGeneric("tau2A.AB<-", function(object, value) standardGeneric("tau2A.AB<-"))
67 64 
 setGeneric("tau2A.BB<-", function(object, value) standardGeneric("tau2A.BB<-"))
68 65 
 setGeneric("tau2B.AA<-", function(object, value) standardGeneric("tau2B.AA<-"))
69 
-##setGeneric("tau2B.AB<-", function(object, value) standardGeneric("tau2B.AB<-"))
70 66 
 setGeneric("tau2B.BB<-", function(object, value) standardGeneric("tau2B.BB<-"))
71 67
72 68 
 setGeneric("corrAA", function(object) standardGeneric("corrAA"))
... ... 
@@ -86,16 +82,12 @@ setGeneric("phiPrimeA", function(object) standardGeneric("phiPrimeA"))
86 82 
 setGeneric("phiPrimeB", function(object) standardGeneric("phiPrimeB"))
87 83 
 setGeneric("phiPrimeA<-", function(object, value) standardGeneric("phiPrimeA<-"))
88 84 
 setGeneric("phiPrimeB<-", function(object, value) standardGeneric("phiPrimeB<-"))
89 
-setGeneric("sigma2A", function(object) standardGeneric("sigma2A"))
90 
-setGeneric("sigma2B", function(object) standardGeneric("sigma2B"))
91 85 
 setGeneric("tau2A", function(object) standardGeneric("tau2A"))
92 86 
 setGeneric("tau2B", function(object) standardGeneric("tau2B"))
93 87 
 setGeneric("nuA<-", function(object, value) standardGeneric("nuA<-"))
94 88 
 setGeneric("nuB<-", function(object, value) standardGeneric("nuB<-"))
95 89 
 setGeneric("phiA<-", function(object, value) standardGeneric("phiA<-"))
96 90 
 setGeneric("phiB<-", function(object, value) standardGeneric("phiB<-"))
97 
-setGeneric("sigma2A<-", function(object, value) standardGeneric("sigma2A<-"))
98 
-setGeneric("sigma2B<-", function(object, value) standardGeneric("sigma2B<-"))
99 91 
 setGeneric("tau2A<-", function(object, value) standardGeneric("tau2A<-"))
100 92 
 setGeneric("tau2B<-", function(object, value) standardGeneric("tau2B<-"))
101 93 
 setGeneric("flags<-", function(object, value) standardGeneric("flags<-"))
Browse code

Removed tryCatch() statements in readIdatFiles. Restored previous implementation.

Added statements to illumina_copynumber.Rnw that make use of checkExists function.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49126 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:19
Showing 1 changed files
R/AllGenerics.R
History View file @ f1e14c0
... ... 
@@ -101,3 +101,4 @@ setGeneric("tau2B<-", function(object, value) standardGeneric("tau2B<-"))
101 101 
 setGeneric("flags<-", function(object, value) standardGeneric("flags<-"))
102 102
103 103
104 
+
Browse code

Added citation to crlmmCopynumber. Deleted many of the commented functions in cnrma-functions.R

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48963 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:50:15
Showing 1 changed files
R/AllGenerics.R
History View file @ 6b75ec7
... ... 
@@ -2,14 +2,14 @@
2 2 
 ##setGeneric("getParam", function(object, name, batch) standardGeneric("getParam"))
3 3 
 setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
4 4 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
5 
-setGeneric("computeCopynumber", function(object, ...) standardGeneric("computeCopynumber"))
5 
+##setGeneric("computeCopynumber", function(object, ...) standardGeneric("computeCopynumber"))
6 6 
 ##setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
7 7 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
8 8 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
9 9
10 10 
 setGeneric("CA", function(object, ...) standardGeneric("CA"))
11 11 
 setGeneric("CB", function(object, ...) standardGeneric("CB"))
12 
-##setGeneric("totalCopyNumber", function(object, ...) standardGeneric("totalCopyNumber"))
12 
+setGeneric("totalCopynumber", function(object, ...) standardGeneric("totalCopynumber"))
13 13
14 14
15 15 
 setGeneric("Ns", function(object, ...) standardGeneric("Ns"))
Browse code

Numerous changed to copy number estimation detailed below.

Added the following functions:
o summarizeMaleXGenotypes
- impute genotype 'A' and genotype 'B' location when unobserved
- shrink within genotype variances
o shrinkGenotypeSummaries
- impute unobserved genotype 'AA', 'AB' and 'BB' genotypes
- shrink within genotype variances
o summarizeSnps
- within genotype location and scale. Genotype frequencies
o summarizeNps
- location and scale at nonpolymorphic loci
o genotypeSummary
- wrapper for summarizeSnps and summarizeNps

Extensively edited the following functions:
o fit.lm1 - fit.lm4
(these functions only fit the linear model to the within/genotype location scale)

Requires oligoClasses 1.11.7

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48959 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:49:54
Showing 1 changed files
R/AllGenerics.R
History View file @ 6846d58
... ... 
@@ -12,19 +12,84 @@ setGeneric("CB", function(object, ...) standardGeneric("CB"))
12 12 
 ##setGeneric("totalCopyNumber", function(object, ...) standardGeneric("totalCopyNumber"))
13 13
14 14
15 
+setGeneric("Ns", function(object, ...) standardGeneric("Ns"))
16 
+setGeneric("corr", function(object, ...) standardGeneric("corr"))
17 
+setGeneric("mads", function(object, ...) standardGeneric("mads"))
18 
+setGeneric("medians", function(object, ...) standardGeneric("medians"))
19 
+setGeneric("tau2", function(object, ...) standardGeneric("tau2"))
20 
+
15 21 
 ## The generics below are for internal use with copy number methods
16 22 
 ## If we keep them in oligoClasses, we need to export and document
23 
+setGeneric("N.AA", function(object) standardGeneric("N.AA"))
24 
+setGeneric("N.AB", function(object) standardGeneric("N.AB"))
25 
+setGeneric("N.BB", function(object) standardGeneric("N.BB"))
26 
+setGeneric("N.AA<-", function(object, value) standardGeneric("N.AA<-"))
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+setGeneric("N.AB<-", function(object, value) standardGeneric("N.AB<-"))
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+setGeneric("N.BB<-", function(object, value) standardGeneric("N.BB<-"))
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+
30 
+setGeneric("medians", function(object, ...) standardGeneric("medians"))
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+setGeneric("medianA.AA", function(object) standardGeneric("medianA.AA"))
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+setGeneric("medianA.AB", function(object) standardGeneric("medianA.AB"))
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+setGeneric("medianA.BB", function(object) standardGeneric("medianA.BB"))
34 
+setGeneric("medianB.AA", function(object) standardGeneric("medianB.AA"))
35 
+setGeneric("medianB.AB", function(object) standardGeneric("medianB.AB"))
36 
+setGeneric("medianB.BB", function(object) standardGeneric("medianB.BB"))
37 
+setGeneric("medianA.AA<-", function(object, value) standardGeneric("medianA.AA<-"))
38 
+setGeneric("medianA.AB<-", function(object, value) standardGeneric("medianA.AB<-"))
39 
+setGeneric("medianA.BB<-", function(object, value) standardGeneric("medianA.BB<-"))
40 
+setGeneric("medianB.AA<-", function(object, value) standardGeneric("medianB.AA<-"))
41 
+setGeneric("medianB.AB<-", function(object, value) standardGeneric("medianB.AB<-"))
42 
+setGeneric("medianB.BB<-", function(object, value) standardGeneric("medianB.BB<-"))
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+
44 
+
45 
+
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+setGeneric("madA.AA", function(object) standardGeneric("madA.AA"))
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+setGeneric("madA.AB", function(object) standardGeneric("madA.AB"))
48 
+setGeneric("madA.BB", function(object) standardGeneric("madA.BB"))
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+setGeneric("madB.AA", function(object) standardGeneric("madB.AA"))
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+setGeneric("madB.AB", function(object) standardGeneric("madB.AB"))
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+setGeneric("madB.BB", function(object) standardGeneric("madB.BB"))
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+setGeneric("madA.AA<-", function(object, value) standardGeneric("madA.AA<-"))
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+setGeneric("madA.AB<-", function(object, value) standardGeneric("madA.AB<-"))
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+setGeneric("madA.BB<-", function(object, value) standardGeneric("madA.BB<-"))
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+setGeneric("madB.AA<-", function(object, value) standardGeneric("madB.AA<-"))
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+setGeneric("madB.AB<-", function(object, value) standardGeneric("madB.AB<-"))
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+setGeneric("madB.BB<-", function(object, value) standardGeneric("madB.BB<-"))
58 
+
59 
+setGeneric("tau2A.AA", function(object) standardGeneric("tau2A.AA"))
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+##setGeneric("tau2A.AB", function(object) standardGeneric("tau2A.AB"))
61 
+setGeneric("tau2A.BB", function(object) standardGeneric("tau2A.BB"))
62 
+setGeneric("tau2B.AA", function(object) standardGeneric("tau2B.AA"))
63 
+##setGeneric("tau2B.AB", function(object) standardGeneric("tau2B.AB"))
64 
+setGeneric("tau2B.BB", function(object) standardGeneric("tau2B.BB"))
65 
+setGeneric("tau2A.AA<-", function(object, value) standardGeneric("tau2A.AA<-"))
66 
+##setGeneric("tau2A.AB<-", function(object, value) standardGeneric("tau2A.AB<-"))
67 
+setGeneric("tau2A.BB<-", function(object, value) standardGeneric("tau2A.BB<-"))
68 
+setGeneric("tau2B.AA<-", function(object, value) standardGeneric("tau2B.AA<-"))
69 
+##setGeneric("tau2B.AB<-", function(object, value) standardGeneric("tau2B.AB<-"))
70 
+setGeneric("tau2B.BB<-", function(object, value) standardGeneric("tau2B.BB<-"))
71 
+
72 
+setGeneric("corrAA", function(object) standardGeneric("corrAA"))
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+setGeneric("corrAB", function(object) standardGeneric("corrAB"))
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+setGeneric("corrBB", function(object) standardGeneric("corrBB"))
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+setGeneric("corrAA<-", function(object, value) standardGeneric("corrAA<-"))
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+setGeneric("corrAB<-", function(object, value) standardGeneric("corrAB<-"))
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+setGeneric("corrBB<-", function(object, value) standardGeneric("corrBB<-"))
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+
79 
+
80 
+
17 81 
 setGeneric("nuA", function(object) standardGeneric("nuA"))
18 82 
 setGeneric("nuB", function(object) standardGeneric("nuB"))
19 83 
 setGeneric("phiA", function(object) standardGeneric("phiA"))
20 84 
 setGeneric("phiB", function(object) standardGeneric("phiB"))
85 
+setGeneric("phiPrimeA", function(object) standardGeneric("phiPrimeA"))
86 
+setGeneric("phiPrimeB", function(object) standardGeneric("phiPrimeB"))
87 
+setGeneric("phiPrimeA<-", function(object, value) standardGeneric("phiPrimeA<-"))
88 
+setGeneric("phiPrimeB<-", function(object, value) standardGeneric("phiPrimeB<-"))
21 89 
 setGeneric("sigma2A", function(object) standardGeneric("sigma2A"))
22 90 
 setGeneric("sigma2B", function(object) standardGeneric("sigma2B"))
23 91 
 setGeneric("tau2A", function(object) standardGeneric("tau2A"))
24 92 
 setGeneric("tau2B", function(object) standardGeneric("tau2B"))
25 
-setGeneric("corrAA", function(object) standardGeneric("corrAA"))
26 
-setGeneric("corrBB", function(object) standardGeneric("corrBB"))
27 
-setGeneric("corrAB", function(object) standardGeneric("corrAB"))
28 93 
 setGeneric("nuA<-", function(object, value) standardGeneric("nuA<-"))
29 94 
 setGeneric("nuB<-", function(object, value) standardGeneric("nuB<-"))
30 95 
 setGeneric("phiA<-", function(object, value) standardGeneric("phiA<-"))
... ... 
@@ -33,11 +98,6 @@ setGeneric("sigma2A<-", function(object, value) standardGeneric("sigma2A<-"))
33 98 
 setGeneric("sigma2B<-", function(object, value) standardGeneric("sigma2B<-"))
34 99 
 setGeneric("tau2A<-", function(object, value) standardGeneric("tau2A<-"))
35 100 
 setGeneric("tau2B<-", function(object, value) standardGeneric("tau2B<-"))
36 
-setGeneric("corrAA<-", function(object, value) standardGeneric("corrAA<-"))
37 
-setGeneric("corrAB<-", function(object, value) standardGeneric("corrAB<-"))
38 
-setGeneric("corrBB<-", function(object, value) standardGeneric("corrBB<-"))
39 101 
 setGeneric("flags<-", function(object, value) standardGeneric("flags<-"))
40 102
41 
-setGeneric("numberGenotype<-", function(object, value, ...) standardGeneric("numberGenotype<-"))
42 
-
43 103
Browse code

A number of changes to fit.lm1 and crlmmCopynumber. The number of genotypes is now stored as part of the CNSet class object.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48958 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:49:47
Showing 1 changed files
R/AllGenerics.R
History View file @ d08acba
... ... 
@@ -36,5 +36,8 @@ setGeneric("tau2B<-", function(object, value) standardGeneric("tau2B<-"))
36 36 
 setGeneric("corrAA<-", function(object, value) standardGeneric("corrAA<-"))
37 37 
 setGeneric("corrAB<-", function(object, value) standardGeneric("corrAB<-"))
38 38 
 setGeneric("corrBB<-", function(object, value) standardGeneric("corrBB<-"))
39 
+setGeneric("flags<-", function(object, value) standardGeneric("flags<-"))
40 
+
41 
+setGeneric("numberGenotype<-", function(object, value, ...) standardGeneric("numberGenotype<-"))
39 42
40 43
Browse code

Added help files for copy number accessors. Fixed bugs in CA, CB, and total copy number methods.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48951 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:49:14
Showing 1 changed files
R/AllGenerics.R
History View file @ 69ec864
... ... 
@@ -7,11 +7,9 @@ setGeneric("computeCopynumber", function(object, ...) standardGeneric("computeCo
7 7 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
8 8 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
9 9
10 
-setGeneric("totalCopyNumber", function(object,...) standardGeneric("totalCopyNumber"))
11 
-
12 
-setGeneric("CA", function(object, i, j, ...) standardGeneric("CA"))
13 
-setGeneric("CB", function(object, i, j, ...) standardGeneric("CB"))
14 
-setGeneric("totalCopyNumber", function(object, i, j, ...) standardGeneric("totalCopyNumber"))
10 
+setGeneric("CA", function(object, ...) standardGeneric("CA"))
11 
+setGeneric("CB", function(object, ...) standardGeneric("CB"))
12 
+##setGeneric("totalCopyNumber", function(object, ...) standardGeneric("totalCopyNumber"))
15 13
16 14
17 15 
 ## The generics below are for internal use with copy number methods
Browse code

Updated sample.CNSetLM helpfile with coercion to v1.0.1 of the CNSet class definition

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48950 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:49:06
Showing 1 changed files
R/AllGenerics.R
History View file @ 8160162
... ... 
@@ -16,14 +16,8 @@ setGeneric("totalCopyNumber", function(object, i, j, ...) standardGeneric("total
16 16
17 17 
 ## The generics below are for internal use with copy number methods
18 18 
 ## If we keep them in oligoClasses, we need to export and document
19 
-setGeneric("corr", function(object, allele) standardGeneric("corr"))
20 
-setGeneric("nu", function(object, allele) standardGeneric("nu"))
21 
-setGeneric("phi", function(object, allele) standardGeneric("phi"))
22 
-setGeneric("sigma2", function(object, allele) standardGeneric("sigma2"))
23 
-setGeneric("tau2", function(object, allele) standardGeneric("tau2"))
24 
-
25 19 
 setGeneric("nuA", function(object) standardGeneric("nuA"))
26 
-setGeneric("nuB", function(object) standardGeneric("nuA"))
20 
+setGeneric("nuB", function(object) standardGeneric("nuB"))
27 21 
 setGeneric("phiA", function(object) standardGeneric("phiA"))
28 22 
 setGeneric("phiB", function(object) standardGeneric("phiB"))
29 23 
 setGeneric("sigma2A", function(object) standardGeneric("sigma2A"))
... ... 
@@ -33,7 +27,6 @@ setGeneric("tau2B", function(object) standardGeneric("tau2B"))
33 27 
 setGeneric("corrAA", function(object) standardGeneric("corrAA"))
34 28 
 setGeneric("corrBB", function(object) standardGeneric("corrBB"))
35 29 
 setGeneric("corrAB", function(object) standardGeneric("corrAB"))
36 
-
37 30 
 setGeneric("nuA<-", function(object, value) standardGeneric("nuA<-"))
38 31 
 setGeneric("nuB<-", function(object, value) standardGeneric("nuB<-"))
39 32 
 setGeneric("phiA<-", function(object, value) standardGeneric("phiA<-"))
Browse code

Added methods for LinearModelParameter class. removed methods for SnpSuperSet class.

Added a lot of generics for accessing and updating elements in the
LinearModelParameter class.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48949 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:48:57
Showing 1 changed files
R/AllGenerics.R
History View file @ 97e84a8
... ... 
@@ -1,23 +1,49 @@
1 
-setGeneric("batch", function(object) standardGeneric("batch"))
2 
-setGeneric("getParam", function(object, name, batch) standardGeneric("getParam"))
1 
+##setGeneric("batch", function(object) standardGeneric("batch"))
2 
+##setGeneric("getParam", function(object, name, batch) standardGeneric("getParam"))
3 3 
 setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
4 4 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
5 5 
 setGeneric("computeCopynumber", function(object, ...) standardGeneric("computeCopynumber"))
6 
-setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
6 
+##setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
7 7 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
8 8 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
9 
-setGeneric("lM", function(object) standardGeneric("lM"))
10 
-setGeneric("lM<-", function(object, value) standardGeneric("lM<-"))
9 
+
11 10 
 setGeneric("totalCopyNumber", function(object,...) standardGeneric("totalCopyNumber"))
12 11
12 
+setGeneric("CA", function(object, i, j, ...) standardGeneric("CA"))
13 
+setGeneric("CB", function(object, i, j, ...) standardGeneric("CB"))
14 
+setGeneric("totalCopyNumber", function(object, i, j, ...) standardGeneric("totalCopyNumber"))
15 
+
16 
+
17 
+## The generics below are for internal use with copy number methods
18 
+## If we keep them in oligoClasses, we need to export and document
13 19 
 setGeneric("corr", function(object, allele) standardGeneric("corr"))
14 20 
 setGeneric("nu", function(object, allele) standardGeneric("nu"))
15 21 
 setGeneric("phi", function(object, allele) standardGeneric("phi"))
16 22 
 setGeneric("sigma2", function(object, allele) standardGeneric("sigma2"))
17 23 
 setGeneric("tau2", function(object, allele) standardGeneric("tau2"))
18 24
19 
-setGeneric("CA", function(object, i, j, ...) standardGeneric("CA"))
20 
-setGeneric("CB", function(object, i, j, ...) standardGeneric("CB"))
21 
-setGeneric("totalCopyNumber", function(object, i, j, ...) standardGeneric("totalCopyNumber"))
25 
+setGeneric("nuA", function(object) standardGeneric("nuA"))
26 
+setGeneric("nuB", function(object) standardGeneric("nuA"))
27 
+setGeneric("phiA", function(object) standardGeneric("phiA"))
28 
+setGeneric("phiB", function(object) standardGeneric("phiB"))
29 
+setGeneric("sigma2A", function(object) standardGeneric("sigma2A"))
30 
+setGeneric("sigma2B", function(object) standardGeneric("sigma2B"))
31 
+setGeneric("tau2A", function(object) standardGeneric("tau2A"))
32 
+setGeneric("tau2B", function(object) standardGeneric("tau2B"))
33 
+setGeneric("corrAA", function(object) standardGeneric("corrAA"))
34 
+setGeneric("corrBB", function(object) standardGeneric("corrBB"))
35 
+setGeneric("corrAB", function(object) standardGeneric("corrAB"))
36 
+
37 
+setGeneric("nuA<-", function(object, value) standardGeneric("nuA<-"))
38 
+setGeneric("nuB<-", function(object, value) standardGeneric("nuB<-"))
39 
+setGeneric("phiA<-", function(object, value) standardGeneric("phiA<-"))
40 
+setGeneric("phiB<-", function(object, value) standardGeneric("phiB<-"))
41 
+setGeneric("sigma2A<-", function(object, value) standardGeneric("sigma2A<-"))
42 
+setGeneric("sigma2B<-", function(object, value) standardGeneric("sigma2B<-"))
43 
+setGeneric("tau2A<-", function(object, value) standardGeneric("tau2A<-"))
44 
+setGeneric("tau2B<-", function(object, value) standardGeneric("tau2B<-"))
45 
+setGeneric("corrAA<-", function(object, value) standardGeneric("corrAA<-"))
46 
+setGeneric("corrAB<-", function(object, value) standardGeneric("corrAB<-"))
47 
+setGeneric("corrBB<-", function(object, value) standardGeneric("corrBB<-"))
22 48
23 49
Browse code

Changed generic for CA and CB to include index i for markers and index j for samples

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48939 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:48:17
Showing 1 changed files
R/AllGenerics.R
History View file @ 2c958cf
... ... 
@@ -16,8 +16,8 @@ setGeneric("phi", function(object, allele) standardGeneric("phi"))
16 16 
 setGeneric("sigma2", function(object, allele) standardGeneric("sigma2"))
17 17 
 setGeneric("tau2", function(object, allele) standardGeneric("tau2"))
18 18
19 
-setGeneric("CA", function(object) standardGeneric("CA"))
20 
-setGeneric("CB", function(object) standardGeneric("CB"))
19 
+setGeneric("CA", function(object, i, j, ...) standardGeneric("CA"))
20 
+setGeneric("CB", function(object, i, j, ...) standardGeneric("CB"))
21 21 
 setGeneric("totalCopyNumber", function(object, i, j, ...) standardGeneric("totalCopyNumber"))
22 22
23 23
Browse code

added generics for CA, CB, and totalCopyNumber (moved from oligoClasses)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48938 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:48:14
Showing 1 changed files
R/AllGenerics.R
History View file @ 481f470
... ... 
@@ -16,4 +16,8 @@ setGeneric("phi", function(object, allele) standardGeneric("phi"))
16 16 
 setGeneric("sigma2", function(object, allele) standardGeneric("sigma2"))
17 17 
 setGeneric("tau2", function(object, allele) standardGeneric("tau2"))
18 18
19 
+setGeneric("CA", function(object) standardGeneric("CA"))
20 
+setGeneric("CB", function(object) standardGeneric("CB"))
21 
+setGeneric("totalCopyNumber", function(object, i, j, ...) standardGeneric("totalCopyNumber"))
22 
+
19 23
Browse code

Added accessors for linear model parameters.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48922 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:47:15
Showing 1 changed files
R/AllGenerics.R
History View file @ 518a290
... ... 
@@ -10,4 +10,10 @@ setGeneric("lM", function(object) standardGeneric("lM"))
10 10 
 setGeneric("lM<-", function(object, value) standardGeneric("lM<-"))
11 11 
 setGeneric("totalCopyNumber", function(object,...) standardGeneric("totalCopyNumber"))
12 12
13 
+setGeneric("corr", function(object, allele) standardGeneric("corr"))
14 
+setGeneric("nu", function(object, allele) standardGeneric("nu"))
15 
+setGeneric("phi", function(object, allele) standardGeneric("phi"))
16 
+setGeneric("sigma2", function(object, allele) standardGeneric("sigma2"))
17 
+setGeneric("tau2", function(object, allele) standardGeneric("tau2"))
18 
+
13 19
Browse code

removed plotCNSetLM function and plot method. Added linesCNSetLM function and lines method.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48617 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 02/08/2010 08:51:48
Showing 1 changed files
R/AllGenerics.R
History View file @ b9ad9e2
... ... 
@@ -10,3 +10,4 @@ setGeneric("lM", function(object) standardGeneric("lM"))
10 10 
 setGeneric("lM<-", function(object, value) standardGeneric("lM<-"))
11 11 
 setGeneric("totalCopyNumber", function(object,...) standardGeneric("totalCopyNumber"))
12 12
13 
+
Browse code

Manually removed conflicts with my branch and Matt Ritchie's commit that had a bug fig for v 1.7.6

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48613 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 02/08/2010 08:51:34
Showing 1 changed files
R/AllGenerics.R
History View file @ adde216
... ... 
@@ -8,4 +8,5 @@ setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
8 8 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
9 9 
 setGeneric("lM", function(object) standardGeneric("lM"))
10 10 
 setGeneric("lM<-", function(object, value) standardGeneric("lM<-"))
11 
+setGeneric("totalCopyNumber", function(object,...) standardGeneric("totalCopyNumber"))
11 12
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
Showing 1 changed files
R/AllGenerics.R
History View file @ d5bc779
... ... 
@@ -1,3 +1,4 @@
1 
+setGeneric("batch", function(object) standardGeneric("batch"))
1 2 
 setGeneric("getParam", function(object, name, batch) standardGeneric("getParam"))
2 3 
 setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
3 4 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
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
Showing 1 changed files
R/AllGenerics.R
History View file @ c00f715
... ... 
@@ -1,6 +1,3 @@
1 
-##setGeneric("A<-", function(object, value) standardGeneric("A<-"))
2 
-##setGeneric("B<-", function(object, value) standardGeneric("B<-"))
3 
-
4 1 
 setGeneric("getParam", function(object, name, batch) standardGeneric("getParam"))
5 2 
 setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
6 3 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
... ... 
@@ -8,5 +5,6 @@ setGeneric("computeCopynumber", function(object, ...) standardGeneric("computeCo
8 5 
 setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
9 6 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
10 7 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
11 
-##setGeneric("splitByChromosome", function(object, ...) standardGeneric("splitByChromosome"))
8 
+setGeneric("lM", function(object) standardGeneric("lM"))
9 
+setGeneric("lM<-", function(object, value) standardGeneric("lM<-"))
12 10
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
Showing 1 changed files
R/AllGenerics.R
History View file @ 1c2a3f4
... ... 
@@ -4,7 +4,7 @@
4 4 
 setGeneric("getParam", function(object, name, batch) standardGeneric("getParam"))
5 5 
 setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
6 6 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
7 
-setGeneric("computeCopynumber", function(object, cnOptions) standardGeneric("computeCopynumber"))
7 
+setGeneric("computeCopynumber", function(object, ...) standardGeneric("computeCopynumber"))
8 8 
 setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
9 9 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
10 10 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
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
Showing 1 changed files
R/AllGenerics.R
History View file @ a333524
... ... 
@@ -1,5 +1,3 @@
1 
-setGeneric("A", function(object) standardGeneric("A"))
2 
-setGeneric("B", function(object) standardGeneric("B"))
3 1 
 ##setGeneric("A<-", function(object, value) standardGeneric("A<-"))
4 2 
 ##setGeneric("B<-", function(object, value) standardGeneric("B<-"))
5 3
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
R/AllGenerics.R
History View file @ 5fcfed7
... ... 
@@ -1,57 +1,14 @@
1 
-setGeneric("A<-", function(object, value) standardGeneric("A<-"))
2 
-setGeneric("B<-", function(object, value) standardGeneric("B<-"))
1 
+setGeneric("A", function(object) standardGeneric("A"))
2 
+setGeneric("B", function(object) standardGeneric("B"))
3 
+##setGeneric("A<-", function(object, value) standardGeneric("A<-"))
4 
+##setGeneric("B<-", function(object, value) standardGeneric("B<-"))
3 5
4 
-setGeneric("getParam", function(object, name, ...) standardGeneric("getParam"))
6 
+setGeneric("getParam", function(object, name, batch) standardGeneric("getParam"))
5 7 
 setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
6 8 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
7 
-setGeneric("confs", function(object) standardGeneric("confs"))
8 
-setGeneric("computeCopynumber", function(object) standardGeneric("computeCopynumber"))
9 
-setGeneric("crlmm", function(object, ...) standardGeneric("crlmm"))
10 
-setGeneric("crlmmOptions", function(object) standardGeneric("crlmmOptions"))
11 
-setGeneric("crlmmOptions<-", function(object, value) standardGeneric("crlmmOptions<-"))
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-setGeneric("construct", function(object, filenames) standardGeneric("construct"))
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-
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-setGeneric("getOptions", function(object) standardGeneric("getOptions"))
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-
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-##setGeneric("getA", function(object) standardGeneric("getA"))
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-##setGeneric("getB", function(object) standardGeneric("getB"))
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-##setGeneric("getG", function(object) standardGeneric("getG"))
19 
-##setGeneric("getR", function(object) standardGeneric("getR"))
20 
-##setGeneric("getZero", function(object) standardGeneric("getZero"))
21 
-##setGeneric("getCalls", function(object) standardGeneric("getCalls"))
22 
-##setGeneric("getConfs", function(object) standardGeneric("getConfs"))
23 
-##setGeneric("getCA", function(object) standardGeneric("getCA"))
24 
-##setGeneric("getCB", function(object) standardGeneric("getCB"))
25 
-setGeneric("getPhenoData", function(object) standardGeneric("getPhenoData"))
26 
-setGeneric("getFeatureData", function(object) standardGeneric("getFeatureData"))
27 
-setGeneric("getProtocolData", function(object, filenames) standardGeneric("getProtocolData"))
28 
-setGeneric("getGenomeAnnotation", function(object, ...) standardGeneric("getGenomeAnnotation"))
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-setGeneric("getLinearModelParam", function(object, ...) standardGeneric("getLinearModelParam"))
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-
31 
-##setGeneric("initializeStorage", function(object) standardGeneric("initializeStorage"))
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-setGeneric("prediction", function(x, ...) standardGeneric("prediction"))
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-setGeneric("genomeAnnotation", function(object) standardGeneric("genomeAnnotation"))
34 
-setGeneric("genomeAnnotation<-", function(object,value) standardGeneric("genomeAnnotation<-"))
35 
-setGeneric("lM", function(object) standardGeneric("lM"))
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-setGeneric("lM<-", function(object, value) standardGeneric("lM<-"))
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-
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-##setGeneric("nFeatures", function(object) standardGeneric("nFeatures"))
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-
9 
+setGeneric("computeCopynumber", function(object, cnOptions) standardGeneric("computeCopynumber"))
40 10 
 setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
41 
-setGeneric("rma", function(object) standardGeneric("rma"))
42 
-setGeneric("snprma", function(object, ...) standardGeneric("snprma"))
43 11 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
44 12 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
45 13 
 ##setGeneric("splitByChromosome", function(object, ...) standardGeneric("splitByChromosome"))
46 14
47 
-setGeneric("R", function(object) standardGeneric("R"))
48 
-setGeneric("G", function(object) standardGeneric("G"))
49 
-setGeneric("Z", function(object) standardGeneric("Z"))
50 
-setGeneric("X", function(object) standardGeneric("X"))
51 
-setGeneric("Y", function(object) standardGeneric("Y"))
52 
-setMethod("R", "IlluminaRGSet", function(object) assayDataElement(object, "R"))
53 
-setMethod("G", "IlluminaRGSet", function(object) assayDataElement(object, "G"))
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-setMethod("Z", "IlluminaRGSet", function(object) assayDataElement(object, "zero"))
55 
-setMethod("X", "IlluminaXYSet", function(object) assayDataElement(object, "X"))
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-setMethod("Y", "IlluminaXYSet", function(object) assayDataElement(object, "Y"))
57 
-setMethod("Z", "IlluminaXYSet", function(object) assayDataElement(object, "zero"))
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
R/AllGenerics.R
History View file @ a13f66d
... ... 
@@ -1,12 +1,57 @@
1 
-##setGeneric("A<-", function(object, value) standardGeneric("A<-"))
2 
-##setGeneric("B<-", function(object, value) standardGeneric("B<-"))
1 
+setGeneric("A<-", function(object, value) standardGeneric("A<-"))
2 
+setGeneric("B<-", function(object, value) standardGeneric("B<-"))
3 3
4 4 
 setGeneric("getParam", function(object, name, ...) standardGeneric("getParam"))
5 5 
 setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
6 6 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
7 
-setGeneric("computeCopynumber", function(object, cnOptions) standardGeneric("computeCopynumber"))
7 
+setGeneric("confs", function(object) standardGeneric("confs"))
8 
+setGeneric("computeCopynumber", function(object) standardGeneric("computeCopynumber"))
9 
+setGeneric("crlmm", function(object, ...) standardGeneric("crlmm"))
10 
+setGeneric("crlmmOptions", function(object) standardGeneric("crlmmOptions"))
11 
+setGeneric("crlmmOptions<-", function(object, value) standardGeneric("crlmmOptions<-"))
12 
+setGeneric("construct", function(object, filenames) standardGeneric("construct"))
13 
+
14 
+setGeneric("getOptions", function(object) standardGeneric("getOptions"))
15 
+
16 
+##setGeneric("getA", function(object) standardGeneric("getA"))
17 
+##setGeneric("getB", function(object) standardGeneric("getB"))
18 
+##setGeneric("getG", function(object) standardGeneric("getG"))
19 
+##setGeneric("getR", function(object) standardGeneric("getR"))
20 
+##setGeneric("getZero", function(object) standardGeneric("getZero"))
21 
+##setGeneric("getCalls", function(object) standardGeneric("getCalls"))
22 
+##setGeneric("getConfs", function(object) standardGeneric("getConfs"))
23 
+##setGeneric("getCA", function(object) standardGeneric("getCA"))
24 
+##setGeneric("getCB", function(object) standardGeneric("getCB"))
25 
+setGeneric("getPhenoData", function(object) standardGeneric("getPhenoData"))
26 
+setGeneric("getFeatureData", function(object) standardGeneric("getFeatureData"))
27 
+setGeneric("getProtocolData", function(object, filenames) standardGeneric("getProtocolData"))
28 
+setGeneric("getGenomeAnnotation", function(object, ...) standardGeneric("getGenomeAnnotation"))
29 
+setGeneric("getLinearModelParam", function(object, ...) standardGeneric("getLinearModelParam"))
30 
+
31 
+##setGeneric("initializeStorage", function(object) standardGeneric("initializeStorage"))
32 
+setGeneric("prediction", function(x, ...) standardGeneric("prediction"))
33 
+setGeneric("genomeAnnotation", function(object) standardGeneric("genomeAnnotation"))
34 
+setGeneric("genomeAnnotation<-", function(object,value) standardGeneric("genomeAnnotation<-"))
35 
+setGeneric("lM", function(object) standardGeneric("lM"))
36 
+setGeneric("lM<-", function(object, value) standardGeneric("lM<-"))
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+
38 
+##setGeneric("nFeatures", function(object) standardGeneric("nFeatures"))
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+
8 40 
 setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
41 
+setGeneric("rma", function(object) standardGeneric("rma"))
42 
+setGeneric("snprma", function(object, ...) standardGeneric("snprma"))
9 43 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
10 44 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
11 45 
 ##setGeneric("splitByChromosome", function(object, ...) standardGeneric("splitByChromosome"))
12 46
47 
+setGeneric("R", function(object) standardGeneric("R"))
48 
+setGeneric("G", function(object) standardGeneric("G"))
49 
+setGeneric("Z", function(object) standardGeneric("Z"))
50 
+setGeneric("X", function(object) standardGeneric("X"))
51 
+setGeneric("Y", function(object) standardGeneric("Y"))
52 
+setMethod("R", "IlluminaRGSet", function(object) assayDataElement(object, "R"))
53 
+setMethod("G", "IlluminaRGSet", function(object) assayDataElement(object, "G"))
54 
+setMethod("Z", "IlluminaRGSet", function(object) assayDataElement(object, "zero"))
55 
+setMethod("X", "IlluminaXYSet", function(object) assayDataElement(object, "X"))
56 
+setMethod("Y", "IlluminaXYSet", function(object) assayDataElement(object, "Y"))
57 
+setMethod("Z", "IlluminaXYSet", function(object) assayDataElement(object, "zero"))
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
Showing 1 changed files
R/AllGenerics.R
History View file @ 7e1d14d
... ... 
@@ -1,9 +1,7 @@
1 
-setGeneric("A", function(object) standardGeneric("A"))
2 
-setGeneric("B", function(object) standardGeneric("B"))
3 1 
 ##setGeneric("A<-", function(object, value) standardGeneric("A<-"))
4 2 
 ##setGeneric("B<-", function(object, value) standardGeneric("B<-"))
5 3
6 
-setGeneric("getParam", function(object, name, batch) standardGeneric("getParam"))
4 
+setGeneric("getParam", function(object, name, ...) standardGeneric("getParam"))
7 5 
 setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
8 6 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
9 7 
 setGeneric("computeCopynumber", function(object, cnOptions) standardGeneric("computeCopynumber"))
Browse code

removed generics for addFeatureAnnotation and GT<-

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43732 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/12/2009 12:55:31
Showing 1 changed files
R/AllGenerics.R
History View file @ 73436da
... ... 
@@ -1,16 +1,12 @@
1 1 
 setGeneric("A", function(object) standardGeneric("A"))
2 2 
 setGeneric("B", function(object) standardGeneric("B"))
3 
-setGeneric("A<-", function(object, value) standardGeneric("A<-"))
4 
-setGeneric("B<-", function(object, value) standardGeneric("B<-"))
5 
-setGeneric("addFeatureAnnotation", function(object, ...) standardGeneric("addFeatureAnnotation"))
3 
+##setGeneric("A<-", function(object, value) standardGeneric("A<-"))
4 
+##setGeneric("B<-", function(object, value) standardGeneric("B<-"))
6 5
7 6 
 setGeneric("getParam", function(object, name, batch) standardGeneric("getParam"))
8 
-setGeneric("GT<-", function(object, value) standardGeneric("GT<-"))
9 7 
 setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
10 8 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
11 9 
 setGeneric("computeCopynumber", function(object, cnOptions) standardGeneric("computeCopynumber"))
12 
-##setGeneric("GT", function(object, ...) standardGeneric("GT"))
13 
-setGeneric(".harmonizeDimnames", function(object) standardGeneric(".harmonizeDimnames"))
14 10 
 setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
15 11 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
16 12 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
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
Showing 1 changed files
R/AllGenerics.R
History View file @ 7ae22f5
... ... 
@@ -15,3 +15,4 @@ setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
15 15 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
16 16 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
17 17 
 ##setGeneric("splitByChromosome", function(object, ...) standardGeneric("splitByChromosome"))
18 
+
Browse code

updates to namespace, cnrma-functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43541 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 14/12/2009 14:12:43
Showing 1 changed files
R/AllGenerics.R
History View file @ 82be31d
... ... 
@@ -1,31 +1,17 @@
1 1 
 setGeneric("A", function(object) standardGeneric("A"))
2 2 
 setGeneric("B", function(object) standardGeneric("B"))
3 3 
 setGeneric("A<-", function(object, value) standardGeneric("A<-"))
4 
-setGeneric("addFeatureAnnotation", function(object, ...) standardGeneric("addFeatureAnnotation"))
5 4 
 setGeneric("B<-", function(object, value) standardGeneric("B<-"))
5 
+setGeneric("addFeatureAnnotation", function(object, ...) standardGeneric("addFeatureAnnotation"))
6 6
7 
-setGeneric("CA", function(object) standardGeneric("CA"))
8 
-setGeneric("CB", function(object) standardGeneric("CB"))
9 
-setGeneric("CA<-", function(object, value) standardGeneric("CA<-"))
10 
-setGeneric("CB<-", function(object, value) standardGeneric("CB<-"))
11 
-setGeneric("emissionPr", function(object) standardGeneric("emissionPr"))
12 
-setGeneric("emissionPr<-", function(object, value) standardGeneric("emissionPr<-"))
13 7 
 setGeneric("getParam", function(object, name, batch) standardGeneric("getParam"))
14 8 
 setGeneric("GT<-", function(object, value) standardGeneric("GT<-"))
15 9 
 setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
16 10 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
17 11 
 setGeneric("computeCopynumber", function(object, cnOptions) standardGeneric("computeCopynumber"))
18 
-setGeneric("computeEmission", function(object, hmmOptions) standardGeneric("computeEmission"))
19 
-setGeneric("computeHmm", function(object, hmmOptions) standardGeneric("computeHmm"))
20 
-
21 
-setGeneric("GT", function(object, ...) standardGeneric("GT"))
12 
+##setGeneric("GT", function(object, ...) standardGeneric("GT"))
22 13 
 setGeneric(".harmonizeDimnames", function(object) standardGeneric(".harmonizeDimnames"))
23 
-setGeneric("isSnp", function(object) standardGeneric("isSnp"))
24 14 
 setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
25 
-setGeneric("rangedData", function(object) standardGeneric("rangedData"))
26 
-setGeneric("rangedData<-", function(object, value) standardGeneric("rangedData<-"))
27 
-setGeneric("segmentData", function(object) standardGeneric("segmentData"))
28 
-setGeneric("segmentData<-", function(object, value) standardGeneric("segmentData<-"))
29 15 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
30 16 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
31 
-setGeneric("splitByChromosome", function(object, ...) standardGeneric("splitByChromosome"))
17 
+##setGeneric("splitByChromosome", function(object, ...) standardGeneric("splitByChromosome"))
Browse code

updates for compatability with oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43365 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 03/12/2009 13:02:58
Showing 1 changed files
R/AllGenerics.R
History View file @ bc16b51
... ... 
@@ -3,7 +3,7 @@ setGeneric("B", function(object) standardGeneric("B"))
3 3 
 setGeneric("A<-", function(object, value) standardGeneric("A<-"))
4 4 
 setGeneric("addFeatureAnnotation", function(object, ...) standardGeneric("addFeatureAnnotation"))
5 5 
 setGeneric("B<-", function(object, value) standardGeneric("B<-"))
6 
-setGeneric("confs", function(object) standardGeneric("confs"))
6 
+
7 7 
 setGeneric("CA", function(object) standardGeneric("CA"))
8 8 
 setGeneric("CB", function(object) standardGeneric("CB"))
9 9 
 setGeneric("CA<-", function(object, value) standardGeneric("CA<-"))
... ... 
@@ -17,11 +17,13 @@ setGeneric("cnNames", function(object) standardGeneric("cnNames"))
17 17 
 setGeneric("computeCopynumber", function(object, cnOptions) standardGeneric("computeCopynumber"))
18 18 
 setGeneric("computeEmission", function(object, hmmOptions) standardGeneric("computeEmission"))
19 19 
 setGeneric("computeHmm", function(object, hmmOptions) standardGeneric("computeHmm"))
20 
-setGeneric("confs<-", function(object, value) standardGeneric("confs<-"))
20 
+
21 21 
 setGeneric("GT", function(object, ...) standardGeneric("GT"))
22 22 
 setGeneric(".harmonizeDimnames", function(object) standardGeneric(".harmonizeDimnames"))
23 23 
 setGeneric("isSnp", function(object) standardGeneric("isSnp"))
24 24 
 setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
25 
+setGeneric("rangedData", function(object) standardGeneric("rangedData"))
26 
+setGeneric("rangedData<-", function(object, value) standardGeneric("rangedData<-"))
25 27 
 setGeneric("segmentData", function(object) standardGeneric("segmentData"))
26 28 
 setGeneric("segmentData<-", function(object, value) standardGeneric("segmentData<-"))
27 29 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
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
Showing 1 changed files
R/AllGenerics.R
History View file @ bf8acd0
... ... 
@@ -3,20 +3,27 @@ setGeneric("B", function(object) standardGeneric("B"))
3 3 
 setGeneric("A<-", function(object, value) standardGeneric("A<-"))
4 4 
 setGeneric("addFeatureAnnotation", function(object, ...) standardGeneric("addFeatureAnnotation"))
5 5 
 setGeneric("B<-", function(object, value) standardGeneric("B<-"))
6 
-setGeneric("batch", function(object) standardGeneric("batch"))
7 
-##setGeneric("calls", function(x) standardGeneric("calls"))
8 6 
 setGeneric("confs", function(object) standardGeneric("confs"))
9 
-setGeneric("CA", function(object, ...) standardGeneric("CA"))
10 
-setGeneric("CB", function(object, ...) standardGeneric("CB"))
7 
+setGeneric("CA", function(object) standardGeneric("CA"))
8 
+setGeneric("CB", function(object) standardGeneric("CB"))
11 9 
 setGeneric("CA<-", function(object, value) standardGeneric("CA<-"))
12 10 
 setGeneric("CB<-", function(object, value) standardGeneric("CB<-"))
13 
-##setGeneric("chromosome", function(object) standardGeneric("chromosome"))
14 
-setGeneric("cnIndex", function(object, ...) standardGeneric("cnIndex"))
15 
-setGeneric("cnNames", function(object, ...) standardGeneric("cnNames"))
16 
-##setGeneric("copyNumber", function(object) standardGeneric("copyNumber"))
17 
-##setGeneric("position", function(object) standardGeneric("position"))
11 
+setGeneric("emissionPr", function(object) standardGeneric("emissionPr"))
12 
+setGeneric("emissionPr<-", function(object, value) standardGeneric("emissionPr<-"))
13 
+setGeneric("getParam", function(object, name, batch) standardGeneric("getParam"))
14 
+setGeneric("GT<-", function(object, value) standardGeneric("GT<-"))
15 
+setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
16 
+setGeneric("cnNames", function(object) standardGeneric("cnNames"))
17 
+setGeneric("computeCopynumber", function(object, cnOptions) standardGeneric("computeCopynumber"))
18 
+setGeneric("computeEmission", function(object, hmmOptions) standardGeneric("computeEmission"))
19 
+setGeneric("computeHmm", function(object, hmmOptions) standardGeneric("computeHmm"))
20 
+setGeneric("confs<-", function(object, value) standardGeneric("confs<-"))
21 
+setGeneric("GT", function(object, ...) standardGeneric("GT"))
18 22 
 setGeneric(".harmonizeDimnames", function(object) standardGeneric(".harmonizeDimnames"))
19 
-setGeneric("snpIndex", function(object, ...) standardGeneric("snpIndex"))
20 
-setGeneric("snpNames", function(object, ...) standardGeneric("snpNames"))
23 
+setGeneric("isSnp", function(object) standardGeneric("isSnp"))
24 
+setGeneric("pr", function(object, name, batch, value) standardGeneric("pr"))
25 
+setGeneric("segmentData", function(object) standardGeneric("segmentData"))
26 
+setGeneric("segmentData<-", function(object, value) standardGeneric("segmentData<-"))
27 
+setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
28 
+setGeneric("snpNames", function(object) standardGeneric("snpNames"))
21 29 
 setGeneric("splitByChromosome", function(object, ...) standardGeneric("splitByChromosome"))
22 
-
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
R/AllGenerics.R
History View file @ 2ae7850
... ... 
@@ -1,5 +1,8 @@
1 1 
 setGeneric("A", function(object) standardGeneric("A"))
2 2 
 setGeneric("B", function(object) standardGeneric("B"))
3 
+setGeneric("A<-", function(object, value) standardGeneric("A<-"))
4 
+setGeneric("addFeatureAnnotation", function(object, ...) standardGeneric("addFeatureAnnotation"))
5 
+setGeneric("B<-", function(object, value) standardGeneric("B<-"))
3 6 
 setGeneric("batch", function(object) standardGeneric("batch"))
4 7 
 ##setGeneric("calls", function(x) standardGeneric("calls"))
5 8 
 setGeneric("confs", function(object) standardGeneric("confs"))
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
Showing 1 changed files
R/AllGenerics.R
History View file @ 43b13ec
... ... 
@@ -8,12 +8,12 @@ setGeneric("CB", function(object, ...) standardGeneric("CB"))
8 8 
 setGeneric("CA<-", function(object, value) standardGeneric("CA<-"))
9 9 
 setGeneric("CB<-", function(object, value) standardGeneric("CB<-"))
10 10 
 ##setGeneric("chromosome", function(object) standardGeneric("chromosome"))
11 
-setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
12 
-setGeneric("cnNames", function(object) standardGeneric("cnNames"))
11 
+setGeneric("cnIndex", function(object, ...) standardGeneric("cnIndex"))
12 
+setGeneric("cnNames", function(object, ...) standardGeneric("cnNames"))
13 13 
 ##setGeneric("copyNumber", function(object) standardGeneric("copyNumber"))
14 14 
 ##setGeneric("position", function(object) standardGeneric("position"))
15 15 
 setGeneric(".harmonizeDimnames", function(object) standardGeneric(".harmonizeDimnames"))
16 
-setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
17 
-setGeneric("snpNames", function(object) standardGeneric("snpNames"))
16 
+setGeneric("snpIndex", function(object, ...) standardGeneric("snpIndex"))
17 
+setGeneric("snpNames", function(object, ...) standardGeneric("snpNames"))
18 18 
 setGeneric("splitByChromosome", function(object, ...) standardGeneric("splitByChromosome"))
19 19
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
R/AllGenerics.R
History View file @ b9c7172
... ... 
@@ -1,9 +1,10 @@
1 1 
 setGeneric("A", function(object) standardGeneric("A"))
2 2 
 setGeneric("B", function(object) standardGeneric("B"))
3 
+setGeneric("batch", function(object) standardGeneric("batch"))
3 4 
 ##setGeneric("calls", function(x) standardGeneric("calls"))
4 5 
 setGeneric("confs", function(object) standardGeneric("confs"))
5 
-setGeneric("CA", function(object) standardGeneric("CA"))
6 
-setGeneric("CB", function(object) standardGeneric("CB"))
6 
+setGeneric("CA", function(object, ...) standardGeneric("CA"))
7 
+setGeneric("CB", function(object, ...) standardGeneric("CB"))
7 8 
 setGeneric("CA<-", function(object, value) standardGeneric("CA<-"))
8 9 
 setGeneric("CB<-", function(object, value) standardGeneric("CB<-"))
9 10 
 ##setGeneric("chromosome", function(object) standardGeneric("chromosome"))
... ... 
@@ -11,6 +12,7 @@ setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
11 12 
 setGeneric("cnNames", function(object) standardGeneric("cnNames"))
12 13 
 ##setGeneric("copyNumber", function(object) standardGeneric("copyNumber"))
13 14 
 ##setGeneric("position", function(object) standardGeneric("position"))
15 
+setGeneric(".harmonizeDimnames", function(object) standardGeneric(".harmonizeDimnames"))
14 16 
 setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
15 17 
 setGeneric("snpNames", function(object) standardGeneric("snpNames"))
16 18 
 setGeneric("splitByChromosome", function(object, ...) standardGeneric("splitByChromosome"))
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
Showing 1 changed files
R/AllGenerics.R
History View file @ 6446394
... ... 
@@ -1,7 +1,6 @@
1 1 
 setGeneric("A", function(object) standardGeneric("A"))
2 2 
 setGeneric("B", function(object) standardGeneric("B"))
3 3 
 ##setGeneric("calls", function(x) standardGeneric("calls"))
4 
-
5 4 
 setGeneric("confs", function(object) standardGeneric("confs"))
6 5 
 setGeneric("CA", function(object) standardGeneric("CA"))
7 6 
 setGeneric("CB", function(object) standardGeneric("CB"))
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
R/AllGenerics.R
History View file @ 45dab54
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,18 @@
1 
+setGeneric("A", function(object) standardGeneric("A"))
2 
+setGeneric("B", function(object) standardGeneric("B"))
3 
+##setGeneric("calls", function(x) standardGeneric("calls"))
4 
+
5 
+setGeneric("confs", function(object) standardGeneric("confs"))
6 
+setGeneric("CA", function(object) standardGeneric("CA"))
7 
+setGeneric("CB", function(object) standardGeneric("CB"))
8 
+setGeneric("CA<-", function(object, value) standardGeneric("CA<-"))
9 
+setGeneric("CB<-", function(object, value) standardGeneric("CB<-"))
10 
+##setGeneric("chromosome", function(object) standardGeneric("chromosome"))
11 
+setGeneric("cnIndex", function(object) standardGeneric("cnIndex"))
12 
+setGeneric("cnNames", function(object) standardGeneric("cnNames"))
13 
+##setGeneric("copyNumber", function(object) standardGeneric("copyNumber"))
14 
+##setGeneric("position", function(object) standardGeneric("position"))
15 
+setGeneric("snpIndex", function(object) standardGeneric("snpIndex"))
16 
+setGeneric("snpNames", function(object) standardGeneric("snpNames"))
17 
+setGeneric("splitByChromosome", function(object, ...) standardGeneric("splitByChromosome"))
18 
+