Browse code

added code to allow genotype calling for Illumina chips without the need for region specific package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@126739 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 14/02/2017 03:47:52
Showing1 changed files
... ...
@@ -58,10 +58,9 @@ importFrom(mvtnorm, rmvnorm)
58 58
 
59 59
 importFrom(oligoClasses, celfileDate, chromosome2integer, i2p,
60 60
            initializeBigMatrix, initializeBigVector, integerMatrix,
61
-	   isPackageLoaded,
62
-           ldPath, ocLapply, ocProbesets, ocSamples,
63
-	   parStatus,
64
-           splitIndicesByLength, splitIndicesByNode, AssayDataList)
61
+           isPackageLoaded, ldPath, ocLapply, ocProbesets, ocSamples,
62
+           parStatus, splitIndicesByLength, splitIndicesByNode, 
63
+           AssayDataList, genomeBuild, celfileName)
65 64
 
66 65
 importFrom(preprocessCore, normalize.quantiles, normalize.quantiles.determine.target,
67 66
            normalize.quantiles.use.target, subColSummarizeMedian)
... ...
@@ -85,6 +84,8 @@ importFrom(parallel, makeCluster, detectCores, parRapply, stopCluster, clusterEv
85 84
 
86 85
 importFrom(limma, loessFit)
87 86
 
87
+importFrom(ff, delete)
88
+
88 89
 ##----------------------------------------------------------------------------
89 90
 ## export
90 91
 ##----------------------------------------------------------------------------
Browse code

Added nopackage option for krlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117087 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 03/05/2016 23:39:54
Showing1 changed files
... ...
@@ -13,7 +13,7 @@ import(methods)
13 13
 importFrom(RcppEigen, fastLmPure)
14 14
 ## importClassesFrom(oligoClasses, CNSet, CNSetLM, ff_matrix,
15 15
 ##                   ff_or_matrix, oligoSnpSet)
16
-importClassesFrom(oligoClasses, CNSet, oligoSnpSet, ff_or_matrix)
16
+importClassesFrom(oligoClasses, CNSet, oligoSnpSet, ff_or_matrix, GenomeAnnotatedDataFrame)
17 17
 ##setOldClass(ff_or_matrix)
18 18
 import(matrixStats)
19 19
 
... ...
@@ -72,13 +72,18 @@ importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile,
72 72
 importFrom(utils, packageDescription, setTxtProgressBar,
73 73
            txtProgressBar)
74 74
 
75
+importFrom(graphics, plot, smoothScatter, abline)
76
+
77
+importFrom(beanplot, beanplot)
78
+
75 79
 ## foreach
76 80
 import(foreach)
77 81
 
78 82
 importFrom(VGAM, vglm, multinomial, coefficients)
79 83
 
80
-importFrom(parallel, makeCluster, detectCores, parRapply, stopCluster, clusterEvalQ)
84
+importFrom(parallel, makeCluster, detectCores, parRapply, stopCluster, clusterEvalQ, parCapply)
81 85
 
86
+importFrom(limma, loessFit)
82 87
 
83 88
 ##----------------------------------------------------------------------------
84 89
 ## export
... ...
@@ -92,7 +97,6 @@ exportMethods(CA, CB,
92 97
 	      BafLrrSetList)
93 98
 export(crlmm,
94 99
        crlmmIllumina,
95
-       crlmmIlluminaV2,
96 100
        constructAffyCNSet,
97 101
        genotype,
98 102
        genotypeAffy,
... ...
@@ -106,6 +110,7 @@ export(crlmm,
106 110
        genotype2, genotypeLD,
107 111
        genotypeAffy,
108 112
        genotype.Illumina,
113
+       plotSamples, plotSNPs,
109 114
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
110 115
 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
111 116
 export(ABpanel, validCEL, celDates, validCdfNames)
Browse code

Changed tolerance allowed for reading in arrays with different numbers of probes (was 10000, now 4% of total number of probes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@91227 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 10/06/2014 23:43:33
Showing1 changed files
... ...
@@ -77,6 +77,9 @@ import(foreach)
77 77
 
78 78
 importFrom(VGAM, vglm, multinomial, coefficients)
79 79
 
80
+importFrom(parallel, makeCluster, detectCores, parRapply, stopCluster, clusterEvalQ)
81
+
82
+
80 83
 ##----------------------------------------------------------------------------
81 84
 ## export
82 85
 ##----------------------------------------------------------------------------
Browse code

merged matt's changes on the collab branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@86002 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 03/02/2014 14:03:16
Showing1 changed files
... ...
@@ -18,7 +18,7 @@ importClassesFrom(oligoClasses, CNSet, oligoSnpSet, ff_or_matrix)
18 18
 import(matrixStats)
19 19
 
20 20
 importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation,
21
-                  assayData, experimentData, featureData,
21
+                  AnnotatedDataFrame, assayData, experimentData, featureData,
22 22
                   "featureData<-", featureNames, "featureNames<-",
23 23
                   pData, "pData<-", phenoData, "phenoData<-",
24 24
                   protocolData, "protocolData<-",
Browse code

fix conflict in description

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@80947 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/09/2013 14:07:17
Showing1 changed files
... ...
@@ -75,6 +75,8 @@ importFrom(utils, packageDescription, setTxtProgressBar,
75 75
 ## foreach
76 76
 import(foreach)
77 77
 
78
+importFrom(VGAM, vglm, multinomial, coefficients)
79
+
78 80
 ##----------------------------------------------------------------------------
79 81
 ## export
80 82
 ##----------------------------------------------------------------------------
Browse code

merging from collab

* collab:
add warning in vignette about NAs with BafLrrSetList function
Added Human Omni Express Exome 8 v1.1b as a supported chip
updated version number of pacakge and man pages to reflect these changes
skeleton for krlmm capability added. genotype.Illumina() can now take and XY object as input
update copynumber.Rnw to use BafLrrSetList
updates to vignettes
update namespace

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@79138 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 31/07/2013 01:37:34
Showing1 changed files
... ...
@@ -63,7 +63,7 @@ importFrom(oligoClasses, celfileDate, chromosome2integer, i2p,
63 63
 	   parStatus,
64 64
            splitIndicesByLength, splitIndicesByNode, AssayDataList)
65 65
 
66
-importFrom(preprocessCore, normalize.quantiles,
66
+importFrom(preprocessCore, normalize.quantiles, normalize.quantiles.determine.target,
67 67
            normalize.quantiles.use.target, subColSummarizeMedian)
68 68
 
69 69
 importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile,
Browse code

update namespace

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@72808 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/01/2013 05:14:35
Showing1 changed files
... ...
@@ -52,7 +52,7 @@ importFrom(ellipse, ellipse)
52 52
 importFrom(lattice, lpolygon, panel.grid, panel.number, panel.xyplot,
53 53
            xyplot)
54 54
 
55
-importFrom(methods, as, callNextMethod, is, new, validObject)
55
+##importFrom(methods, as, callNextMethod, is, new, validObject)
56 56
 
57 57
 importFrom(mvtnorm, rmvnorm)
58 58
 
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
Showing1 changed files
... ...
@@ -2,20 +2,26 @@ useDynLib("crlmm", .registration=TRUE)
2 2
 
3 3
 importClassesFrom(Biobase, AssayData, eSet)
4 4
 
5
-importClassesFrom(methods, ANY, character, formula, integer, list,
6
-                  matrix, oldClass)
7
-importFrom(methods, setOldClass)
5
+##importClassesFrom(methods, ANY, character, formula, integer, list,
6
+##                  matrix, oldClass)
7
+##importMethodsFrom(methods, initialize, show)
8
+import(methods)
9
+##importFrom(methods, setOldClass)
10
+##importFrom(methods, as, callNextMethod, is, new, validObject)
11
+##importFrom(methods, callNextMethod, new, validObject, coerce)
12
+
8 13
 importFrom(RcppEigen, fastLmPure)
9 14
 ## importClassesFrom(oligoClasses, CNSet, CNSetLM, ff_matrix,
10 15
 ##                   ff_or_matrix, oligoSnpSet)
11 16
 importClassesFrom(oligoClasses, CNSet, oligoSnpSet, ff_or_matrix)
12 17
 ##setOldClass(ff_or_matrix)
18
+import(matrixStats)
13 19
 
14 20
 importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation,
15 21
                   assayData, experimentData, featureData,
16 22
                   "featureData<-", featureNames, "featureNames<-",
17 23
                   pData, "pData<-", phenoData, "phenoData<-",
18
-                  protocolData, "protocolData<-", rowMedians,
24
+                  protocolData, "protocolData<-",
19 25
                   sampleNames, snpCall, "snpCall<-",
20 26
                   snpCallProbability, "snpCallProbability<-",
21 27
                   storageMode, "storageMode<-", varLabels)
... ...
@@ -25,7 +31,7 @@ importMethodsFrom(BiocGenerics, cbind, colnames, Filter, get,
25 31
                   paste, pmax, pmin, rbind, rownames, sapply, setdiff,
26 32
                   table, union, unique)
27 33
 
28
-importMethodsFrom(genefilter, show)
34
+##importMethodsFrom(genefilter, show)
29 35
 
30 36
 importMethodsFrom(oligoClasses, A, "A<-", B, batch, batchNames,
31 37
                   batchStatistics, "batchStatistics<-", calls,
... ...
@@ -34,12 +40,14 @@ importMethodsFrom(oligoClasses, A, "A<-", B, batch, batchNames,
34 40
 
35 41
 importFrom(affyio, read.celfile, read.celfile.header)
36 42
 
43
+importFrom(illuminaio, readIDAT)
44
+
37 45
 importFrom(Biobase, assayDataElement, assayDataElementReplace,
38 46
            assayDataNew, copyEnv)
39 47
 
40 48
 importFrom(ellipse, ellipse)
41 49
 
42
-importFrom(genefilter, rowSds)
50
+##importFrom(genefilter, rowSds)
43 51
 
44 52
 importFrom(lattice, lpolygon, panel.grid, panel.number, panel.xyplot,
45 53
            xyplot)
... ...
@@ -75,14 +83,14 @@ exportMethods(CA, CB,
75 83
 	      A, B, corr, nuA, nuB, phiA, phiB,
76 84
 	      predictionRegion, posteriorProbability,
77 85
 	      tau2, Ns, medians, mads,
78
-	      xyplot, calculateRBaf)
86
+	      xyplot, calculateRBaf, OligoSetList,
87
+	      BafLrrSetList)
79 88
 export(crlmm,
80 89
        crlmmIllumina,
81 90
        crlmmIlluminaV2,
82 91
        constructAffyCNSet,
83 92
        genotype,
84 93
        genotypeAffy,
85
-       readIDAT,
86 94
        readIdatFiles,
87 95
        readGenCallOutput,
88 96
        snprma,
... ...
@@ -96,3 +104,5 @@ export(crlmm,
96 104
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
97 105
 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
98 106
 export(ABpanel, validCEL, celDates, validCdfNames)
107
+
108
+##export(constructOligoSetListFrom, constructBafLrrSetListFrom)
Browse code

@<- has been moved from methods to base, so it no longer needs to be imported in package NAMESPACEs.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@72298 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 04/01/2013 21:18:09
Showing1 changed files
... ...
@@ -44,7 +44,7 @@ importFrom(genefilter, rowSds)
44 44
 importFrom(lattice, lpolygon, panel.grid, panel.number, panel.xyplot,
45 45
            xyplot)
46 46
 
47
-importFrom(methods, "@<-", as, callNextMethod, is, new, validObject)
47
+importFrom(methods, as, callNextMethod, is, new, validObject)
48 48
 
49 49
 importFrom(mvtnorm, rmvnorm)
50 50
 
Browse code

merge with collab branch containing fix for dqrls and bug-fix for computeRBaf that can misalign sample index with batch index (when batch is not in alphabetical order)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@71295 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 17/11/2012 15:24:46
Showing1 changed files
... ...
@@ -5,7 +5,7 @@ importClassesFrom(Biobase, AssayData, eSet)
5 5
 importClassesFrom(methods, ANY, character, formula, integer, list,
6 6
                   matrix, oldClass)
7 7
 importFrom(methods, setOldClass)
8
-
8
+importFrom(RcppEigen, fastLmPure)
9 9
 ## importClassesFrom(oligoClasses, CNSet, CNSetLM, ff_matrix,
10 10
 ##                   ff_or_matrix, oligoSnpSet)
11 11
 importClassesFrom(oligoClasses, CNSet, oligoSnpSet, ff_or_matrix)
... ...
@@ -56,7 +56,7 @@ importFrom(oligoClasses, celfileDate, chromosome2integer, i2p,
56 56
            splitIndicesByLength, splitIndicesByNode, AssayDataList)
57 57
 
58 58
 importFrom(preprocessCore, normalize.quantiles,
59
-           normalize.quantiles.use.target)
59
+           normalize.quantiles.use.target, subColSummarizeMedian)
60 60
 
61 61
 importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile,
62 62
            sd)
Browse code

Merge branch 'collab'

* collab:
Update CNSet objects in data/ with datadir slot and protocolData(object)$filename
update cnrmaAffy. processCEL2 located inside cnrmaAffy function. Uses lexical scope.
Change API for genotypeAffy -- remove mixtureParams argument. Update call to genotypeAffy in genotype function
snprmaAffy no longer initializes mixtureParams object, but accesses this information from the cnSet
constructAffyCNSet initializes mixtureParams slot of the appropriate dimensions
updated cnrmaAffy. Removed cnrma2, cnrma. cnrmaAffy uses lexical scope
Fix bug in crlmmGT2 caused by unequal batch sizes
Moved rsprocessCel inside of snprmaAffy for lexical scope. Moved imputeGender inside crlmmGT2 for lexical scope
Revert imputeGender to original approach for crlmm. Splitting samples across nodes does not work well if there are not a lot of samples in the individual nodes. Probably better to use fewer markers on chr X when large number of samples are processed
contains old process1 call
change gender <- unlist(gender) to gender <- unlist(genderList)
v1.15.15 Fix memory leak in imputeGender step by running this function in sample batches of size ocSamples(). Use lexical scope in calling process1 function in crlmmGT2.
set default values in summarizeNps
depends on v 1.19.39 of oligoClasses
v1.15.14: Export constructAffyCNSet. Used datadir slot in CNSet object added to v 1.19.39 of oligoClasses
update getFeatureData for use with annotation package that contains a number of SNPs not necessarily included in the genotyping. These additional snps are removed when constructing the featureData in constructAffy

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@67826 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/07/2012 03:57:08
Showing1 changed files
... ...
@@ -79,14 +79,19 @@ exportMethods(CA, CB,
79 79
 export(crlmm,
80 80
        crlmmIllumina,
81 81
        crlmmIlluminaV2,
82
+       constructAffyCNSet,
82 83
        genotype,
84
+       genotypeAffy,
83 85
        readIDAT,
84 86
        readIdatFiles,
85 87
        readGenCallOutput,
86 88
        snprma,
87 89
        snprma2,
90
+       cnrmaAffy,
91
+       snprmaAffy,
88 92
        crlmm2,
89 93
        genotype2, genotypeLD,
94
+       genotypeAffy,
90 95
        genotype.Illumina,
91 96
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
92 97
 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
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
Showing1 changed files
... ...
@@ -53,7 +53,7 @@ importFrom(oligoClasses, celfileDate, chromosome2integer, i2p,
53 53
 	   isPackageLoaded,
54 54
            ldPath, ocLapply, ocProbesets, ocSamples,
55 55
 	   parStatus,
56
-           splitIndicesByLength, splitIndicesByNode)
56
+           splitIndicesByLength, splitIndicesByNode, AssayDataList)
57 57
 
58 58
 importFrom(preprocessCore, normalize.quantiles,
59 59
            normalize.quantiles.use.target)
... ...
@@ -64,11 +64,14 @@ importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile,
64 64
 importFrom(utils, packageDescription, setTxtProgressBar,
65 65
            txtProgressBar)
66 66
 
67
+## foreach
68
+import(foreach)
69
+
67 70
 ##----------------------------------------------------------------------------
68 71
 ## export
69 72
 ##----------------------------------------------------------------------------
70 73
 exportClasses(PredictionRegion)
71
-exportMethods(CA, CB, coerce,
74
+exportMethods(CA, CB,
72 75
 	      A, B, corr, nuA, nuB, phiA, phiB,
73 76
 	      predictionRegion, posteriorProbability,
74 77
 	      tau2, Ns, medians, mads,
... ...
@@ -87,4 +90,4 @@ export(crlmm,
87 90
        genotype.Illumina,
88 91
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
89 92
 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
90
-export(ABpanel, validCEL, celDates)
93
+export(ABpanel, validCEL, celDates, validCdfNames)
Browse code

Merge branch 'collab'

* collab:
bump version
made cnSetExample smaller. Fix notes
Trying to revert bad commit
remove cn-functions. update description
comment most of cn-functions.r
Resaved rdas
update data/cnSetExample.rda and data/cnSetExample2.rda
bump version
coercion method from CNSet to oligoSnpSet makes integer matrices of BAFs and lrr's
import ff_or_matrix from oligoClasses. bump dependency on oligoClasses version. Use library(oligoClasses) in some of the crlmm examples.
Cleaning pkg loading process: work still required
move Biobase and methods to imports

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64324 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/03/2012 03:34:50
Showing1 changed files
... ...
@@ -1,56 +1,68 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2 2
 
3
-##---------------------------------------------------------------------------
4
-## Biobase
5
-##---------------------------------------------------------------------------
6
-importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, SnpSet,
7
-		  NChannelSet, MIAME, Versioned, VersionedBiobase,
8
-		  Versions)
9
-importMethodsFrom(Biobase, annotation, "annotation<-",
10
-                  annotatedDataFrameFrom, assayData, "assayData<-",
11
-                  combine, dims, experimentData, "experimentData<-",
12
-                  fData, featureData, "featureData<-", featureNames,
13
-                  fvarMetadata, fvarLabels, pData, "pData<-", phenoData,
14
-                  "phenoData<-", protocolData, "protocolData<-",
15
-                  pubMedIds, rowMedians, sampleNames, snpCall,
16
-                  snpCallProbability,
17
-		  "snpCall<-", "snpCallProbability<-", storageMode,
18
-                  "storageMode<-", updateObject, varLabels)
19
-importFrom(Biobase, assayDataElement, assayDataElementNames,
20
-           assayDataElementReplace, assayDataNew, classVersion,
21
-           validMsg)
22
-
23
-##---------------------------------------------------------------------------
24
-## oligoClasses
25
-##---------------------------------------------------------------------------
26
-importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)##, ff_or_matrix)
27
-importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
28
-		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,
29
-		  chromosome, position, A, B,
30
-		  "A<-", "B<-", open, close, flags,
31
-		  openff, closeff,
32
-		  batchStatistics, "batchStatistics<-", updateObject,
33
-		  checkOrder)
34
-
35
-importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
36
-           copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
37
-
38
-
39
-importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
40
-           polygon, rect, segments, text, points, boxplot, lines)
41
-
42
-importFrom(lattice, xyplot, simpleKey, panel.grid, panel.xyplot, lrect, ltext,
43
-	   lpoints, panel.number, lpolygon)
44
-
45
-importFrom(grDevices, grey)
46
-importFrom(affyio, read.celfile.header, read.celfile)
47
-importFrom(preprocessCore, normalize.quantiles.use.target, normalize.quantiles)
48
-importFrom(utils, data, packageDescription, setTxtProgressBar, txtProgressBar)
49
-importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd, update)
50
-importFrom(genefilter, rowSds)
51
-importFrom(mvtnorm, dmvnorm)
3
+importClassesFrom(Biobase, AssayData, eSet)
4
+
5
+importClassesFrom(methods, ANY, character, formula, integer, list,
6
+                  matrix, oldClass)
7
+importFrom(methods, setOldClass)
8
+
9
+## importClassesFrom(oligoClasses, CNSet, CNSetLM, ff_matrix,
10
+##                   ff_or_matrix, oligoSnpSet)
11
+importClassesFrom(oligoClasses, CNSet, oligoSnpSet, ff_or_matrix)
12
+##setOldClass(ff_or_matrix)
13
+
14
+importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation,
15
+                  assayData, experimentData, featureData,
16
+                  "featureData<-", featureNames, "featureNames<-",
17
+                  pData, "pData<-", phenoData, "phenoData<-",
18
+                  protocolData, "protocolData<-", rowMedians,
19
+                  sampleNames, snpCall, "snpCall<-",
20
+                  snpCallProbability, "snpCallProbability<-",
21
+                  storageMode, "storageMode<-", varLabels)
22
+
23
+importMethodsFrom(BiocGenerics, cbind, colnames, Filter, get,
24
+                  intersect, lapply, ncol, NCOL, nrow, NROW, order,
25
+                  paste, pmax, pmin, rbind, rownames, sapply, setdiff,
26
+                  table, union, unique)
27
+
28
+importMethodsFrom(genefilter, show)
29
+
30
+importMethodsFrom(oligoClasses, A, "A<-", B, batch, batchNames,
31
+                  batchStatistics, "batchStatistics<-", calls,
32
+                  chromosome, close, confs, flags, isSnp, mean, nu,
33
+                  open, phi, "sampleNames<-")
34
+
35
+importFrom(affyio, read.celfile, read.celfile.header)
36
+
37
+importFrom(Biobase, assayDataElement, assayDataElementReplace,
38
+           assayDataNew, copyEnv)
39
+
52 40
 importFrom(ellipse, ellipse)
53
-##importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
41
+
42
+importFrom(genefilter, rowSds)
43
+
44
+importFrom(lattice, lpolygon, panel.grid, panel.number, panel.xyplot,
45
+           xyplot)
46
+
47
+importFrom(methods, "@<-", as, callNextMethod, is, new, validObject)
48
+
49
+importFrom(mvtnorm, rmvnorm)
50
+
51
+importFrom(oligoClasses, celfileDate, chromosome2integer, i2p,
52
+           initializeBigMatrix, initializeBigVector, integerMatrix,
53
+	   isPackageLoaded,
54
+           ldPath, ocLapply, ocProbesets, ocSamples,
55
+	   parStatus,
56
+           splitIndicesByLength, splitIndicesByNode)
57
+
58
+importFrom(preprocessCore, normalize.quantiles,
59
+           normalize.quantiles.use.target)
60
+
61
+importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile,
62
+           sd)
63
+
64
+importFrom(utils, packageDescription, setTxtProgressBar,
65
+           txtProgressBar)
54 66
 
55 67
 ##----------------------------------------------------------------------------
56 68
 ## export
Browse code

Merge branch 'collab'

* collab:
remove getCluster() calls and replace with parStatus()
update man pages for crlmm and genotype.Illumina with respect to the setup for parallelization
add neededPkgs argument to ocLapply calls in crlmmGT2
bump dependency on oligoClasses
Update R/crlmm-illumina.R
contructInf, preprocessInf and genotypeInf no longer exported

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64211 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/03/2012 02:52:50
Showing1 changed files
... ...
@@ -75,4 +75,4 @@ export(crlmm,
75 75
        genotype.Illumina,
76 76
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
77 77
 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
78
-export(ABpanel, constructInf, preprocessInf, genotypeInf, validCEL, celDates)
78
+export(ABpanel, validCEL, celDates)
Browse code

Merge branch 'collab'

* collab:
coercion of CNSet to oligoSnpSet uses lrr/baf instead of ca+cb/genotypes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@62557 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 05/02/2012 15:20:45
Showing1 changed files
... ...
@@ -52,9 +52,15 @@ importFrom(mvtnorm, dmvnorm)
52 52
 importFrom(ellipse, ellipse)
53 53
 ##importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
54 54
 
55
-##importClassesFrom(oligoClasses, ff_matrix, ffdf)
56
-##exportMethods(lines)
57
-exportMethods(CA, CB)
55
+##----------------------------------------------------------------------------
56
+## export
57
+##----------------------------------------------------------------------------
58
+exportClasses(PredictionRegion)
59
+exportMethods(CA, CB, coerce,
60
+	      A, B, corr, nuA, nuB, phiA, phiB,
61
+	      predictionRegion, posteriorProbability,
62
+	      tau2, Ns, medians, mads,
63
+	      xyplot, calculateRBaf)
58 64
 export(crlmm,
59 65
        crlmmIllumina,
60 66
        crlmmIlluminaV2,
... ...
@@ -69,7 +75,4 @@ export(crlmm,
69 75
        genotype.Illumina,
70 76
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
71 77
 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
72
-exportMethods(A, B, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads,
73
-	      xyplot, calculateRBaf)
74 78
 export(ABpanel, constructInf, preprocessInf, genotypeInf, validCEL, celDates)
75
-exportClasses(PredictionRegion)
Browse code

Merge branch 'mymac'

* mymac:
add AffyGW.pdf
update vignettes in inst/scripts
Change argument of validCEL to celfiles
Update constructInf to accommodate GenomeDataFrame class for featureData
bump version to 1.13.7
Add doRUnit.R
Add celfile-utils.Rd
Streamlne some of the Rd files
add validCEL function that checks whether all celfiles can be read
getFeatureData returns GenomeAnnotatedDataFrame
Remove imports from methods. Remove pdf of illumina_copynumber.pdf (large file) and copynumber.pdf
getFeatureDAta returns GenomeAnnotatedDataFrame
Remove separate vignette for copy number in inst/scripts. Include copynumber section in both affy and illumina pipelines.
update documentation files for genotype.Illumina, preprocessInf, and genotypeInf (cdfName added as argument. Indicate that 'batch' should be a character string)
pass cdfName to genotypeInf and preprocessInf
add unitTests and cn-functions for 'simple usage'
Combine AffyPreprocess and copynumber. Combine IlluminaPreprocess and copynumber
remove depency on ff to allow installation on my mac

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@62108 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 17/01/2012 19:13:44
Showing1 changed files
... ...
@@ -1,4 +1,5 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2
+
2 3
 ##---------------------------------------------------------------------------
3 4
 ## Biobase
4 5
 ##---------------------------------------------------------------------------
... ...
@@ -22,7 +23,7 @@ importFrom(Biobase, assayDataElement, assayDataElementNames,
22 23
 ##---------------------------------------------------------------------------
23 24
 ## oligoClasses
24 25
 ##---------------------------------------------------------------------------
25
-importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)
26
+importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)##, ff_or_matrix)
26 27
 importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
27 28
 		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,
28 29
 		  chromosome, position, A, B,
... ...
@@ -49,9 +50,9 @@ importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd, updat
49 50
 importFrom(genefilter, rowSds)
50 51
 importFrom(mvtnorm, dmvnorm)
51 52
 importFrom(ellipse, ellipse)
52
-importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
53
+##importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
53 54
 
54
-importClassesFrom(oligoClasses, ff_matrix, ffdf)
55
+##importClassesFrom(oligoClasses, ff_matrix, ffdf)
55 56
 ##exportMethods(lines)
56 57
 exportMethods(CA, CB)
57 58
 export(crlmm,
... ...
@@ -70,5 +71,5 @@ export(crlmm,
70 71
 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
71 72
 exportMethods(A, B, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads,
72 73
 	      xyplot, calculateRBaf)
73
-export(ABpanel, constructInf, preprocessInf, genotypeInf)
74
+export(ABpanel, constructInf, preprocessInf, genotypeInf, validCEL, celDates)
74 75
 exportClasses(PredictionRegion)
Browse code

remove 'order' from imports in namespace

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@60285 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 14/11/2011 17:49:20
Showing1 changed files
... ...
@@ -29,7 +29,7 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
29 29
 		  "A<-", "B<-", open, close, flags,
30 30
 		  openff, closeff,
31 31
 		  batchStatistics, "batchStatistics<-", updateObject,
32
-		  order, checkOrder)
32
+		  checkOrder)
33 33
 
34 34
 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
35 35
            copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
Browse code

Added man page for readGenCallOutput()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@59152 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 13/10/2011 05:40:07
Showing1 changed files
... ...
@@ -60,6 +60,7 @@ export(crlmm,
60 60
        genotype,
61 61
        readIDAT,
62 62
        readIdatFiles,
63
+       readGenCallOutput,
63 64
        snprma,
64 65
        snprma2,
65 66
        crlmm2,
Browse code

Do not export calculatePosteriorMean

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@59038 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/10/2011 12:17:35
Showing1 changed files
... ...
@@ -67,7 +67,7 @@ export(crlmm,
67 67
        genotype.Illumina,
68 68
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
69 69
 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
70
-exportMethods(A, B, calculatePosteriorMean, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads,
70
+exportMethods(A, B, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads,
71 71
 	      xyplot, calculateRBaf)
72 72
 export(ABpanel, constructInf, preprocessInf, genotypeInf)
73 73
 exportClasses(PredictionRegion)
Browse code

Remove plot-methods. Shorten example for xyplot.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58910 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 08/10/2011 14:07:58
Showing1 changed files
... ...
@@ -52,7 +52,7 @@ importFrom(ellipse, ellipse)
52 52
 importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
53 53
 
54 54
 importClassesFrom(oligoClasses, ff_matrix, ffdf)
55
-exportMethods(lines)
55
+##exportMethods(lines)
56 56
 exportMethods(CA, CB)
57 57
 export(crlmm,
58 58
        crlmmIllumina,
Browse code

crlmm on github

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58751 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2011 16:11:02
Showing1 changed files
... ...
@@ -30,12 +30,14 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
30 30
 		  openff, closeff,
31 31
 		  batchStatistics, "batchStatistics<-", updateObject,
32 32
 		  order, checkOrder)
33
+
33 34
 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
34 35
            copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
35 36
 
36 37
 
37 38
 importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
38 39
            polygon, rect, segments, text, points, boxplot, lines)
40
+
39 41
 importFrom(lattice, xyplot, simpleKey, panel.grid, panel.xyplot, lrect, ltext,
40 42
 	   lpoints, panel.number, lpolygon)
41 43
 
... ...
@@ -48,6 +50,7 @@ importFrom(genefilter, rowSds)
48 50
 importFrom(mvtnorm, dmvnorm)
49 51
 importFrom(ellipse, ellipse)
50 52
 importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
53
+
51 54
 importClassesFrom(oligoClasses, ff_matrix, ffdf)
52 55
 exportMethods(lines)
53 56
 exportMethods(CA, CB)
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
Showing1 changed files
... ...
@@ -64,6 +64,7 @@ export(crlmm,
64 64
        genotype.Illumina,
65 65
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
66 66
 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
67
-exportMethods(A, B, calculatePosteriorMean, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads, xyplot)
67
+exportMethods(A, B, calculatePosteriorMean, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads,
68
+	      xyplot, calculateRBaf)
68 69
 export(ABpanel, constructInf, preprocessInf, genotypeInf)
69 70
 exportClasses(PredictionRegion)
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
Showing1 changed files
... ...
@@ -29,7 +29,7 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
29 29
 		  "A<-", "B<-", open, close, flags,
30 30
 		  openff, closeff,
31 31
 		  batchStatistics, "batchStatistics<-", updateObject,
32
-		  order, checkOrder, snpNames)
32
+		  order, checkOrder)
33 33
 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
34 34
            copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
35 35
 
Browse code

Make API for crlmmGT2 the same as crlmmGT. Define snpNames method for 'character'.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58661 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:50:07
Showing1 changed files
... ...
@@ -29,7 +29,7 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
29 29
 		  "A<-", "B<-", open, close, flags,
30 30
 		  openff, closeff,
31 31
 		  batchStatistics, "batchStatistics<-", updateObject,
32
-		  order, checkOrder)
32
+		  order, checkOrder, snpNames)
33 33
 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
34 34
            copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
35 35
 
Browse code

Add PredictionRegion class that contains 'list'. Export in NAMESPACE. predictionRegion returns PredictionRegion class.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58653 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:49:20
Showing1 changed files
... ...
@@ -28,7 +28,8 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
28 28
 		  chromosome, position, A, B,
29 29
 		  "A<-", "B<-", open, close, flags,
30 30
 		  openff, closeff,
31
-		  batchStatistics, "batchStatistics<-", updateObject)
31
+		  batchStatistics, "batchStatistics<-", updateObject,
32
+		  order, checkOrder)
32 33
 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
33 34
            copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
34 35
 
... ...
@@ -65,3 +66,4 @@ export(crlmm,
65 66
 export(genotypes, totalCopynumber, rawCopynumber, xyplot)
66 67
 exportMethods(A, B, calculatePosteriorMean, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads, xyplot)
67 68
 export(ABpanel, constructInf, preprocessInf, genotypeInf)
69
+exportClasses(PredictionRegion)
Browse code

Simplify accessors for batch summaries: Ns, corr, medians, mads

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58646 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:48:38
Showing1 changed files
... ...
@@ -27,6 +27,7 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
27 27
 		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,
28 28
 		  chromosome, position, A, B,
29 29
 		  "A<-", "B<-", open, close, flags,
30
+		  openff, closeff,
30 31
 		  batchStatistics, "batchStatistics<-", updateObject)
31 32
 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
32 33
            copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
... ...
@@ -46,21 +47,7 @@ importFrom(genefilter, rowSds)
46 47
 importFrom(mvtnorm, dmvnorm)
47 48
 importFrom(ellipse, ellipse)
48 49
 importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
49
-## It is important not to import these classes from oligoClasses
50
-## Doing so causes the following errors:
51
-## N.AA(container)[index, ] <- someMatrix
52
-##Error in function (classes, fdef, mtable)  :
53
-##  unable to find an inherited method for function "medianA.AA<-", for signature "CNSet", "ff_matrix"
54
-##importClassesFrom(oligoClasses, ffdf, ff_matrix)
55 50
 importClassesFrom(oligoClasses, ff_matrix, ffdf)
56
-## Important to export these classes
57
-##exportClasses(ff_or_matrix, ff_matrix, ffdf)
58
-##exportClasses(ff_or_matrix)
59
-##---------------------------------------------------------------------------
60
-## lattice imports
61
-##---------------------------------------------------------------------------
62
-##import(panel.number, panel.grid, panel.xyplot, lpoints, lsegments, lrect, ltext)
63
-
64 51
 exportMethods(lines)
65 52
 exportMethods(CA, CB)
66 53
 export(crlmm,
Browse code

Import lattice and several lattice methods. Export ABpanel function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58636 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:47:29
Showing1 changed files
... ...
@@ -34,6 +34,8 @@ importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
34 34
 
35 35
 importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
36 36
            polygon, rect, segments, text, points, boxplot, lines)
37
+importFrom(lattice, xyplot, simpleKey, panel.grid, panel.xyplot, lrect, ltext,
38
+	   lpoints, panel.number, lpolygon)
37 39
 
38 40
 importFrom(grDevices, grey)
39 41
 importFrom(affyio, read.celfile.header, read.celfile)
... ...
@@ -59,7 +61,6 @@ importClassesFrom(oligoClasses, ff_matrix, ffdf)
59 61
 ##---------------------------------------------------------------------------
60 62
 ##import(panel.number, panel.grid, panel.xyplot, lpoints, lsegments, lrect, ltext)
61 63
 
62
-
63 64
 exportMethods(lines)
64 65
 exportMethods(CA, CB)
65 66
 export(crlmm,
... ...
@@ -74,6 +75,6 @@ export(crlmm,
74 75
        genotype2, genotypeLD,
75 76
        genotype.Illumina,
76 77
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
77
-export(genotypes, totalCopynumber, rawCopynumber)
78
-exportMethods(A, B, calculatePosteriorMean, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads)
79
-export(constructInf, preprocessInf, genotypeInf)
78
+export(genotypes, totalCopynumber, rawCopynumber, xyplot)
79
+exportMethods(A, B, calculatePosteriorMean, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads, xyplot)
80
+export(ABpanel, constructInf, preprocessInf, genotypeInf)
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
Showing1 changed files
... ...
@@ -74,6 +74,6 @@ export(crlmm,
74 74
        genotype2, genotypeLD,
75 75
        genotype.Illumina,
76 76
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
77
-export(totalCopynumber, rawCopynumber)
78
-exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
77
+export(genotypes, totalCopynumber, rawCopynumber)
78
+exportMethods(A, B, calculatePosteriorMean, corr, nuA, nuB, phiA, phiB, predictionRegion, posteriorProbability, tau2, Ns, medians, mads)
79 79
 export(constructInf, preprocessInf, genotypeInf)
Browse code

Export low-level processing function readIDAT() (as requested by Kasper Daniel Hansen)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@56864 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 21/07/2011 04:29:31
Showing1 changed files
... ...
@@ -66,6 +66,7 @@ export(crlmm,
66 66
        crlmmIllumina,
67 67
        crlmmIlluminaV2,
68 68
        genotype,
69
+       readIDAT,
69 70
        readIdatFiles,
70 71
        snprma,
71 72
        snprma2,
Browse code

Remove constructIlluminaCNSet from exports

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@54378 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 02/04/2011 16:52:49
Showing1 changed files
... ...
@@ -73,7 +73,6 @@ export(crlmm,
73 73
        genotype2, genotypeLD,
74 74
        genotype.Illumina,
75 75
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
76
-export(constructIlluminaCNSet)
77 76
 export(totalCopynumber, rawCopynumber)
78 77
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
79 78
 export(constructInf, preprocessInf, genotypeInf)
Browse code

make gender an ff object in genotype function for Affy

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@54170 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/03/2011 02:40:42
Showing1 changed files
... ...
@@ -54,6 +54,12 @@ importClassesFrom(oligoClasses, ff_matrix, ffdf)
54 54
 ## Important to export these classes
55 55
 ##exportClasses(ff_or_matrix, ff_matrix, ffdf)
56 56
 ##exportClasses(ff_or_matrix)
57
+##---------------------------------------------------------------------------
58
+## lattice imports
59
+##---------------------------------------------------------------------------
60
+##import(panel.number, panel.grid, panel.xyplot, lpoints, lsegments, lrect, ltext)
61
+
62
+
57 63
 exportMethods(lines)
58 64
 exportMethods(CA, CB)
59 65
 export(crlmm,
Browse code

Rewrote illumina_copynumber vignette. Add functions and docmentation for constructInf, preprocessInf, and genotypeInf.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@54164 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/03/2011 02:40:07
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... ...
@@ -70,4 +70,4 @@ export(crlmm,
70 70
 export(constructIlluminaCNSet)
71 71
 export(totalCopynumber, rawCopynumber)
72 72
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
73
-
73
+export(constructInf, preprocessInf, genotypeInf)
Browse code

add scale.sd option to computePosteriorMeans

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53848 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 18/03/2011 01:57:07
Showing1 changed files
... ...
@@ -71,10 +71,3 @@ export(constructIlluminaCNSet)
71 71
 export(totalCopynumber, rawCopynumber)
72 72
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
73 73
 
74
-## for posterior means
75
-
76
-
77
-
78
-
79
-
80
-##export(summarizeNps, genotypeSummary, fit.lm2)
Browse code

Remove export of posteriorMean methods in namespace. Comment some debugging code in genotypeIllumina

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53578 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2011 19:30:58
Showing1 changed files
... ...
@@ -72,8 +72,7 @@ export(totalCopynumber, rawCopynumber)
72 72
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
73 73
 
74 74
 ## for posterior means
75
-export(calculatePosteriorMean)
76
-exportMethods(posteriorMean, "posteriorMean<-")
75
+
77 76
 
78 77
 
79 78
 
Browse code

Create the function rawCopynumber that aliases totalCopynumber

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53577 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2011 19:30:54
Showing1 changed files
... ...
@@ -68,7 +68,7 @@ export(crlmm,
68 68
        genotype.Illumina,
69 69
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
70 70
 export(constructIlluminaCNSet)
71
-export(totalCopynumber)
71
+export(totalCopynumber, rawCopynumber)
72 72
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
73 73
 
74 74
 ## for posterior means
Browse code

add scale.sd option to computePosteriorMeans

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53576 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2011 19:30:48
Showing1 changed files
... ...
@@ -71,5 +71,11 @@ export(constructIlluminaCNSet)
71 71
 export(totalCopynumber)
72 72
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
73 73
 
74
+## for posterior means
75
+export(calculatePosteriorMean)
76
+exportMethods(posteriorMean, "posteriorMean<-")
77
+
78
+
79
+
74 80
 
75 81
 ##export(summarizeNps, genotypeSummary, fit.lm2)
Browse code

commit after bioc rebase

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52859 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 16:19:11
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... ...
@@ -1,7 +1,4 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2
-## this is temporary
3
-exportPattern("^[^\\.]")
4
-
5 2
 ##---------------------------------------------------------------------------
6 3
 ## Biobase
7 4
 ##---------------------------------------------------------------------------
Browse code

try splitIndicesByLength instead of splitIndicesByNode in genotype.Illumina

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52849 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:59:12
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... ...
@@ -1,6 +1,6 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2 2
 ## this is temporary
3
- exportPattern("^[^\\.]")
3
+exportPattern("^[^\\.]")
4 4
 
5 5
 ##---------------------------------------------------------------------------
6 6
 ## Biobase
... ...
@@ -68,7 +68,7 @@ export(crlmm,
68 68
        snprma2,
69 69
        crlmm2,
70 70
        genotype2, genotypeLD,
71
-       genotype.Illumina, 
71
+       genotype.Illumina,
72 72
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
73 73
 export(constructIlluminaCNSet)
74 74
 export(totalCopynumber)
Browse code

export everything in namespace

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52841 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:58:43
Showing1 changed files
... ...
@@ -1,6 +1,6 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2 2
 ## this is temporary
3
-## exportPattern("^[^\\.]")
3
+ exportPattern("^[^\\.]")
4 4
 
5 5
 ##---------------------------------------------------------------------------
6 6
 ## Biobase
Browse code

Finalize updates to copynumber and illumina_copynumber vignettes for v1.8.3 updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52837 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:58:28
Showing1 changed files
... ...
@@ -1,6 +1,6 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2 2
 ## this is temporary
3
- exportPattern("^[^\\.]")
3
+## exportPattern("^[^\\.]")
4 4
 
5 5
 ##---------------------------------------------------------------------------
6 6
 ## Biobase
Browse code

update processCEL2 -- only read intensities for NP probes that are included in the npProbesFid object

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52809 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 16/02/2011 15:56:39
Showing1 changed files
... ...
@@ -1,6 +1,6 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2 2
 ## this is temporary
3
-## exportPattern("^[^\\.]")
3
+ exportPattern("^[^\\.]")
4 4
 
5 5
 ##---------------------------------------------------------------------------
6 6
 ## Biobase
Browse code

Cleaning up... importing isPackageLoaded() from oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@51994 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 20/01/2011 18:33:39
Showing1 changed files
... ...
@@ -32,7 +32,7 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
32 32
 		  "A<-", "B<-", open, close, flags,
33 33
 		  batchStatistics, "batchStatistics<-", updateObject)
34 34
 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
35
-           copyNumber, initializeBigMatrix, initializeBigVector)
35
+           copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
36 36
 
37 37
 
38 38
 importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
Browse code

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

unknown authored on 18/11/2010 05:31:36
Showing1 changed files
... ...
@@ -68,6 +68,7 @@ export(crlmm,
68 68
        snprma2,
69 69
        crlmm2,
70 70
        genotype2, genotypeLD,
71
+       genotype.Illumina, 
71 72
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
72 73
 export(constructIlluminaCNSet)
73 74
 export(totalCopynumber)
Browse code

Finalize updates to copynumber and illumina_copynumber vignettes for v1.8.3 updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50890 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/11/2010 14:22:42
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... ...
@@ -1,6 +1,6 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2 2
 ## this is temporary
3
- exportPattern("^[^\\.]")
3
+## exportPattern("^[^\\.]")
4 4
 
5 5
 ##---------------------------------------------------------------------------
6 6
 ## Biobase
Browse code

update processCEL2 -- only read intensities for NP probes that are included in the npProbesFid object

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50884 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 15/11/2010 14:21:23
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... ...
@@ -1,6 +1,6 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2 2
 ## this is temporary
3
-## exportPattern("^[^\\.]")
3
+ exportPattern("^[^\\.]")
4 4
 
5 5
 ##---------------------------------------------------------------------------
6 6
 ## Biobase
Browse code

Bumped version.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50809 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/11/2010 04:13:40
Showing1 changed files
... ...
@@ -1,6 +1,6 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2 2
 ## this is temporary
3
- exportPattern("^[^\\.]")
3
+## exportPattern("^[^\\.]")
4 4
 
5 5
 ##---------------------------------------------------------------------------
6 6
 ## Biobase
Browse code

genotype function should be independent of annotation package version

no longer uses ffrowapply. Updates assayData elements of callSet column by column

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50807 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/11/2010 04:13:23
Showing1 changed files
... ...
@@ -1,6 +1,6 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2 2
 ## this is temporary
3
-## exportPattern("^[^\\.]")
3
+ exportPattern("^[^\\.]")
4 4
 
5 5
 ##---------------------------------------------------------------------------
6 6
 ## Biobase
Browse code

Bug fix for estimation of copy number at nonpolymorphic loci on chromosome X.

Other changes:

- the default threshold for the confidence threshold (GT.CONF.THR) is
now 0.8

- fixed a bug in fit.lm4 that resulted in nans and Inf for nuA and
phiA at nonpolymorphic markers on chromosome X.

- uncommented code in the ACN function to calculate copy number at
nonpolymorphic loci on chromosome X. Seems to be working for both
men and women.

- Added suggestions to the vignette for exploring the missing value
pattern. Most often this will likely be due to the genotype
confidence threshold

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50805 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/11/2010 04:13:08
Showing1 changed files
... ...
@@ -1,6 +1,6 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2 2
 ## this is temporary
3
-exportPattern("^[^\\.]")
3
+## exportPattern("^[^\\.]")
4 4
 
5 5
 ##---------------------------------------------------------------------------
6 6
 ## Biobase
Browse code

getFeatureData only returns features with chromosome annotation

Exclude 232 SNPs returned by getVarInEnv("gns") that are not annotated
to a chromosome.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50804 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/11/2010 04:13:03
Showing1 changed files
... ...
@@ -1,6 +1,6 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2 2
 ## this is temporary
3
-## exportPattern("^[^\\.]")
3
+exportPattern("^[^\\.]")
4 4
 
5 5
 ##---------------------------------------------------------------------------
6 6
 ## Biobase
Browse code

import ffdf class from oligoClasses

- fix warning during install that ffdf was defined with slot oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50356 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 20/10/2010 13:43:26
Showing1 changed files
... ...
@@ -53,7 +53,7 @@ importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
53 53
 ##Error in function (classes, fdef, mtable)  :
54 54
 ##  unable to find an inherited method for function "medianA.AA<-", for signature "CNSet", "ff_matrix"
55 55
 ##importClassesFrom(oligoClasses, ffdf, ff_matrix)
56
-importClassesFrom(oligoClasses, ff_matrix)
56
+importClassesFrom(oligoClasses, ff_matrix, ffdf)
57 57
 ## Important to export these classes
58 58
 ##exportClasses(ff_or_matrix, ff_matrix, ffdf)
59 59
 ##exportClasses(ff_or_matrix)
Browse code

Update summarizeNps function for illumina platform

- A scatterplot of the A and B channels at nonpolymophic loci shows
that one channel appears to be background and the other channel
appears to be signal.

- A quick fix for CN estimation is to replace the normalized
intensities at nonpolymorphic loci for the A allele with the average
from both channels on the intensity scale ((A+B)/2)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@50353 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 20/10/2010 13:43:06
Showing1 changed files
... ...
@@ -74,4 +74,4 @@ export(totalCopynumber)
74 74
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
75 75
 
76 76
 
77
-
77
+##export(summarizeNps, genotypeSummary, fit.lm2)
Browse code

Remove help file for ffdf-class. Adding documentation for CNSet accessors.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49896 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2010 02:21:59
Showing1 changed files
... ...
@@ -1,13 +1,13 @@
1 1
 useDynLib("crlmm", .registration=TRUE)
2
-
3 2
 ## this is temporary
4 3
 ## exportPattern("^[^\\.]")
5 4
 
5
+##---------------------------------------------------------------------------
6 6
 ## Biobase
7
+##---------------------------------------------------------------------------
7 8
 importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, SnpSet,
8 9
 		  NChannelSet, MIAME, Versioned, VersionedBiobase,
9 10
 		  Versions)
10
-
11 11
 importMethodsFrom(Biobase, annotation, "annotation<-",
12 12
                   annotatedDataFrameFrom, assayData, "assayData<-",
13 13
                   combine, dims, experimentData, "experimentData<-",
... ...
@@ -18,21 +18,19 @@ importMethodsFrom(Biobase, annotation, "annotation<-",
18 18
                   snpCallProbability,
19 19
 		  "snpCall<-", "snpCallProbability<-", storageMode,
20 20
                   "storageMode<-", updateObject, varLabels)
21
-
22 21
 importFrom(Biobase, assayDataElement, assayDataElementNames,
23 22
            assayDataElementReplace, assayDataNew, classVersion,
24 23
            validMsg)
25 24
 
25
+##---------------------------------------------------------------------------
26 26
 ## oligoClasses
27
+##---------------------------------------------------------------------------
27 28
 importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)
28
-
29 29
 importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
30 30
 		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,
31 31
 		  chromosome, position, A, B,
32 32
 		  "A<-", "B<-", open, close, flags,
33 33
 		  batchStatistics, "batchStatistics<-", updateObject)
34
-
35
-
36 34
 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
37 35
            copyNumber, initializeBigMatrix, initializeBigVector)
38 36
 
... ...
@@ -41,21 +39,13 @@ importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
41 39
            polygon, rect, segments, text, points, boxplot, lines)
42 40
 
43 41
 importFrom(grDevices, grey)
44
-
45 42
 importFrom(affyio, read.celfile.header, read.celfile)
46
-
47 43
 importFrom(preprocessCore, normalize.quantiles.use.target, normalize.quantiles)
48
-
49 44
 importFrom(utils, data, packageDescription, setTxtProgressBar, txtProgressBar)
50
-
51 45
 importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd, update)
52
-
53 46
 importFrom(genefilter, rowSds)
54
-
55 47
 importFrom(mvtnorm, dmvnorm)
56
-
57 48
 importFrom(ellipse, ellipse)
58
-
59 49
 importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
60 50
 ## It is important not to import these classes from oligoClasses
61 51
 ## Doing so causes the following errors:
... ...
@@ -64,7 +54,6 @@ importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
64 54
 ##  unable to find an inherited method for function "medianA.AA<-", for signature "CNSet", "ff_matrix"
65 55
 ##importClassesFrom(oligoClasses, ffdf, ff_matrix)
66 56
 importClassesFrom(oligoClasses, ff_matrix)
67
-
68 57
 ## Important to export these classes
69 58
 ##exportClasses(ff_or_matrix, ff_matrix, ffdf)
70 59
 ##exportClasses(ff_or_matrix)
... ...
@@ -73,7 +62,6 @@ exportMethods(CA, CB)
73 62
 export(crlmm,
74 63
        crlmmIllumina,
75 64
        crlmmIlluminaV2,
76
-##       ellipseCenters,
77 65
        genotype,
78 66
        readIdatFiles,
79 67
        snprma,
... ...
@@ -83,17 +71,7 @@ export(crlmm,
83 71
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
84 72
 export(constructIlluminaCNSet)
85 73
 export(totalCopynumber)
86
-export(cnrma, cnrma2)
87 74
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
88
-##export(genotypeSummary,
89
-##       shrinkSummary,
90
-##       estimateCnParameters,
91
-##       shrinkGenotypeSummaries,
92
-##       summarizeSnps,
93
-##       constructIlluminaAssayData,
94
-##       ACN, C1, C2, C3)
95
-## For debugging
96
-## exportPattern("^[^\\.]")
97 75
 
98 76
 
99 77
 
Browse code

importing ff_matrix class from oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49144 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:41:12
Showing1 changed files
... ...
@@ -57,17 +57,17 @@ importFrom(mvtnorm, dmvnorm)
57 57
 importFrom(ellipse, ellipse)
58 58
 
59 59
 importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
60
-
61 60
 ## It is important not to import these classes from oligoClasses
62 61
 ## Doing so causes the following errors:
63 62
 ## N.AA(container)[index, ] <- someMatrix
64 63
 ##Error in function (classes, fdef, mtable)  :
65 64
 ##  unable to find an inherited method for function "medianA.AA<-", for signature "CNSet", "ff_matrix"
66 65
 ##importClassesFrom(oligoClasses, ffdf, ff_matrix)
66
+importClassesFrom(oligoClasses, ff_matrix)
67 67
 
68 68
 ## Important to export these classes
69 69
 ##exportClasses(ff_or_matrix, ff_matrix, ffdf)
70
-exportClasses(ff_or_matrix)
70
+##exportClasses(ff_or_matrix)
71 71
 exportMethods(lines)
72 72
 exportMethods(CA, CB)
73 73
 export(crlmm,
... ...
@@ -85,13 +85,13 @@ export(constructIlluminaCNSet)
85 85
 export(totalCopynumber)
86 86
 export(cnrma, cnrma2)
87 87
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
88
-export(genotypeSummary,
89
-       shrinkSummary,
88
+##export(genotypeSummary,
89
+##       shrinkSummary,
90 90
 ##       estimateCnParameters,
91 91
 ##       shrinkGenotypeSummaries,
92 92
 ##       summarizeSnps,
93 93
 ##       constructIlluminaAssayData,
94
-       ACN, C1, C2, C3)
94
+##       ACN, C1, C2, C3)
95 95
 ## For debugging
96 96
 ## exportPattern("^[^\\.]")
97 97
 
Browse code

more pruning of NAMESPACE

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49143 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:41:10
Showing1 changed files
... ...
@@ -73,7 +73,7 @@ exportMethods(CA, CB)
73 73
 export(crlmm,
74 74
        crlmmIllumina,
75 75
        crlmmIlluminaV2,
76
-       ellipseCenters,
76
+##       ellipseCenters,
77 77
        genotype,
78 78
        readIdatFiles,
79 79
        snprma,
... ...
@@ -87,10 +87,11 @@ export(cnrma, cnrma2)
87 87
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
88 88
 export(genotypeSummary,
89 89
        shrinkSummary,
90
-       estimateCnParameters,
91
-       shrinkGenotypeSummaries,
92
-       summarizeSnps,
93
-       constructIlluminaAssayData, ACN, C1, C2, C3)
90
+##       estimateCnParameters,
91
+##       shrinkGenotypeSummaries,
92
+##       summarizeSnps,
93
+##       constructIlluminaAssayData,
94
+       ACN, C1, C2, C3)
94 95
 ## For debugging
95 96
 ## exportPattern("^[^\\.]")
96 97
 
Browse code

cleaned some of the temporary exports in the namespace

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49142 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:41:08
Showing1 changed files
... ...
@@ -89,16 +89,8 @@ export(genotypeSummary,
89 89
        shrinkSummary,
90 90
        estimateCnParameters,
91 91
        shrinkGenotypeSummaries,
92
-##       indexComplete,
93 92
        summarizeSnps,
94
-       constructIlluminaAssayData,
95
-       ACN, C1, C2, C3, fit.lm3,
96
-       linesCNSet)
97
-
98
-exportMethods(N.AA, N.AB, N.BB, "N.AA<-", "N.AB<-", "N.BB<-", medianA.AA, "medianA.AA<-")
99
-
100
-## export(fit.lm1, fit.lm2, fit.lm3, fit.lm4)
101
-
93
+       constructIlluminaAssayData, ACN, C1, C2, C3)
102 94
 ## For debugging
103 95
 ## exportPattern("^[^\\.]")
104 96
 
Browse code

Revised accesors in methods-AssayData -- some of the conflicts resolved by hand during rebase were incorrect

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49140 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:41:03
Showing1 changed files
... ...
@@ -56,7 +56,7 @@ importFrom(mvtnorm, dmvnorm)
56 56
 
57 57
 importFrom(ellipse, ellipse)
58 58
 
59
-importFrom(ff, ffdf, physical.ff, physical.ffdf)
59
+importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
60 60
 
61 61
 ## It is important not to import these classes from oligoClasses
62 62
 ## Doing so causes the following errors:
... ...
@@ -66,7 +66,8 @@ importFrom(ff, ffdf, physical.ff, physical.ffdf)
66 66
 ##importClassesFrom(oligoClasses, ffdf, ff_matrix)
67 67
 
68 68
 ## Important to export these classes
69
-exportClasses(ff_or_matrix, ff_matrix, ffdf)
69
+##exportClasses(ff_or_matrix, ff_matrix, ffdf)
70
+exportClasses(ff_or_matrix)
70 71
 exportMethods(lines)
71 72
 exportMethods(CA, CB)
72 73
 export(crlmm,
Browse code

CB estimates were NA for SNP indices were mixed with NP indices. Bug was fixed in the ACN function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49136 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:54
Showing1 changed files
... ...
@@ -87,7 +87,12 @@ exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
87 87
 export(genotypeSummary,
88 88
        shrinkSummary,
89 89
        estimateCnParameters,
90
-       shrinkGenotypeSummaries, indexComplete, summarizeSnps, constructIlluminaAssayData, crlmmIlluminaV2, ACN, C1, C2, C3, fit.lm3)
90
+       shrinkGenotypeSummaries,
91
+##       indexComplete,
92
+       summarizeSnps,
93
+       constructIlluminaAssayData,
94
+       ACN, C1, C2, C3, fit.lm3,
95
+       linesCNSet)
91 96
 
92 97
 exportMethods(N.AA, N.AB, N.BB, "N.AA<-", "N.AB<-", "N.BB<-", medianA.AA, "medianA.AA<-")
93 98
 
Browse code

Fixed several bugs in the CA, CB, ACN functions. Updated the copynumber vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49132 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:42
Showing1 changed files
... ...
@@ -56,18 +56,25 @@ importFrom(mvtnorm, dmvnorm)
56 56
 
57 57
 importFrom(ellipse, ellipse)
58 58
 
59
-
60
-importFrom(ff, ffdf)
61
-
62
-exportClasses(CNSetLM, ffdf, list)
63
-exportMethods(open, "[", show, lM, plot)
64
-export(crlmm, 
65
-       crlmmCopynumber, 
66
-       crlmmIllumina, 
67
-##       ellipse, 
68
-       genotype, 
69
-       readIdatFiles, 
70
-       readIdatFiles2,
59
+importFrom(ff, ffdf, physical.ff, physical.ffdf)
60
+
61
+## It is important not to import these classes from oligoClasses
62
+## Doing so causes the following errors:
63
+## N.AA(container)[index, ] <- someMatrix
64
+##Error in function (classes, fdef, mtable)  :
65
+##  unable to find an inherited method for function "medianA.AA<-", for signature "CNSet", "ff_matrix"
66
+##importClassesFrom(oligoClasses, ffdf, ff_matrix)
67
+
68
+## Important to export these classes
69
+exportClasses(ff_or_matrix, ff_matrix, ffdf)
70
+exportMethods(lines)
71
+exportMethods(CA, CB)
72
+export(crlmm,
73
+       crlmmIllumina,
74
+       crlmmIlluminaV2,
75
+       ellipseCenters,
76
+       genotype,
77
+       readIdatFiles,
71 78
        snprma,
72 79
        snprma2,
73 80
        crlmm2,
... ...
@@ -80,7 +87,10 @@ exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
80 87
 export(genotypeSummary,
81 88
        shrinkSummary,
82 89
        estimateCnParameters,
83
-       shrinkGenotypeSummaries, indexComplete)
90
+       shrinkGenotypeSummaries, indexComplete, summarizeSnps, constructIlluminaAssayData, crlmmIlluminaV2, ACN, C1, C2, C3, fit.lm3)
91
+
92
+exportMethods(N.AA, N.AB, N.BB, "N.AA<-", "N.AB<-", "N.BB<-", medianA.AA, "medianA.AA<-")
93
+
84 94
 ## export(fit.lm1, fit.lm2, fit.lm3, fit.lm4)
85 95
 
86 96
 ## For debugging
Browse code

constructIlluminaAssayData allows for either ff or matrices. Fixed bug in accessors for medians, mads, ...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49131 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:33
Showing1 changed files
... ...
@@ -71,13 +71,20 @@ export(crlmm,
71 71
        snprma,
72 72
        snprma2,
73 73
        crlmm2,
74
-       genotype2,
75
-       batch,
76
-       crlmmCopynumber2,
77
-       constructCNSetForIllumina,
78
-       validCdfNames)
79
-##export(initializeParamObject, biasAdjNP2)
80
-##export(construct)
81
-
82
-export(plotCNSetLM)
74
+       genotype2, genotypeLD,
75
+       crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
76
+export(constructIlluminaCNSet)
77
+export(totalCopynumber)
78
+export(cnrma, cnrma2)
79
+exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
80
+export(genotypeSummary,
81
+       shrinkSummary,
82
+       estimateCnParameters,
83
+       shrinkGenotypeSummaries, indexComplete)
84
+## export(fit.lm1, fit.lm2, fit.lm3, fit.lm4)
85
+
86
+## For debugging
87
+## exportPattern("^[^\\.]")
88
+
89
+
83 90
 
Browse code

Export plotCNSetLM for debugging.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49130 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:28
Showing1 changed files
... ...
@@ -56,23 +56,11 @@ importFrom(mvtnorm, dmvnorm)
56 56
 
57 57
 importFrom(ellipse, ellipse)
58 58
 
59
-<<<<<<< HEAD
60
-importFrom(ff, ffdf, physical.ff, physical.ffdf)
61
-importClassesFrom(oligoClasses, ffdf, ff_matrix)
62
-
63
-exportMethods(lines)
64
-exportMethods(CA, CB)
65
-export(crlmm,
66
-       crlmmIllumina,
67
-       crlmmIlluminaV2,
68
-       ellipseCenters,
69
-       genotype,
70
-       readIdatFiles,
71
-=======
59
+
72 60
 importFrom(ff, ffdf)
73 61
 
74 62
 exportClasses(CNSetLM, ffdf, list)
75
-exportMethods(open, "[", show, lM)
63
+exportMethods(open, "[", show, lM, plot)
76 64
 export(crlmm, 
77 65
        crlmmCopynumber, 
78 66
        crlmmIllumina, 
... ...
@@ -80,22 +68,16 @@ export(crlmm,
80 68
        genotype, 
81 69
        readIdatFiles, 
82 70
        readIdatFiles2,
83
->>>>>>> Exporting list and ffdf classes so that lM<- assignment works
84 71
        snprma,
85 72
        snprma2,
86 73
        crlmm2,
87
-       genotype2, genotypeLD,
88
-       crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
89
-export(constructIlluminaCNSet)
90
-export(totalCopynumber)
91
-export(cnrma, cnrma2)
92
-exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
93
-export(genotypeSummary,
94
-       shrinkSummary,
95
-       estimateCnParameters)
96
-
97
-## For debugging
98
-## exportPattern("^[^\\.]")
99
-
100
-
74
+       genotype2,
75
+       batch,
76
+       crlmmCopynumber2,
77
+       constructCNSetForIllumina,
78
+       validCdfNames)
79
+##export(initializeParamObject, biasAdjNP2)
80
+##export(construct)
81
+
82
+export(plotCNSetLM)
101 83
 
Browse code

Exporting list and ffdf classes so that lM<- assignment works

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49125 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:40:16
Showing1 changed files
... ...
@@ -56,6 +56,7 @@ importFrom(mvtnorm, dmvnorm)
56 56
 
57 57
 importFrom(ellipse, ellipse)
58 58
 
59
+<<<<<<< HEAD
59 60
 importFrom(ff, ffdf, physical.ff, physical.ffdf)
60 61
 importClassesFrom(oligoClasses, ffdf, ff_matrix)
61 62
 
... ...
@@ -67,6 +68,19 @@ export(crlmm,
67 68
        ellipseCenters,
68 69
        genotype,
69 70
        readIdatFiles,
71
+=======
72
+importFrom(ff, ffdf)
73
+
74
+exportClasses(CNSetLM, ffdf, list)
75
+exportMethods(open, "[", show, lM)
76
+export(crlmm, 
77
+       crlmmCopynumber, 
78
+       crlmmIllumina, 
79
+##       ellipse, 
80
+       genotype, 
81
+       readIdatFiles, 
82
+       readIdatFiles2,
83
+>>>>>>> Exporting list and ffdf classes so that lM<- assignment works
70 84
        snprma,
71 85
        snprma2,
72 86
        crlmm2,
Browse code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49010 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 25/08/2010 02:32:48
Showing1 changed files
... ...
@@ -63,11 +63,10 @@ exportMethods(lines)
63 63
 exportMethods(CA, CB)
64 64
 export(crlmm,
65 65
        crlmmIllumina,
66
-       crlmmIllumina2,
66
+       crlmmIlluminaV2,
67 67
        ellipseCenters,
68 68
        genotype,
69 69
        readIdatFiles,
70
-       readIdatFiles2,
71 70
        snprma,
72 71
        snprma2,
73 72
        crlmm2,
Browse code

methods Ns, medians, corr, and mads return arrays.

Ns and corr return an array with dimension: features x genotype x batch

medians and mads return an array with dimension: features x allele x genotype x batch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48964 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:50:19
Showing1 changed files
... ...
@@ -76,7 +76,7 @@ export(crlmm,
76 76
 export(constructIlluminaCNSet)
77 77
 export(totalCopynumber)
78 78
 export(cnrma, cnrma2)
79
-exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns)
79
+exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
80 80
 export(genotypeSummary,
81 81
        shrinkSummary,
82 82
        estimateCnParameters)
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
Showing1 changed files
... ...
@@ -74,19 +74,12 @@ export(crlmm,
74 74
        genotype2, genotypeLD,
75 75
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
76 76
 export(constructIlluminaCNSet)
77
-##export(linesCNSet)
78
-##export(fit.lm1, fit.lm2, fit.lm3, fit.lm4, construct,
79
-##       dqrlsWrapper, fit.wls)
80
-export(computeCopynumber, totalCopynumber)
77
+export(totalCopynumber)
81 78
 export(cnrma, cnrma2)
82 79
 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns)
83 80
 export(genotypeSummary,
84 81
        shrinkSummary,
85 82
        estimateCnParameters)
86
-##       summarizeSnps,
87
-##       summarizeNps,
88
-##       shrinkGenotypeSummaries,
89
-##       summarizeMaleXGenotypes
90 83
 
91 84
 ## For debugging
92 85
 ## exportPattern("^[^\\.]")
Browse code

Changed totalCopyNumber to totalCopynumber to be consistent with caps in crlmmCopynumber. Fixed a few bugs in the .Rd files

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48962 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:50:10
Showing1 changed files
... ...
@@ -75,18 +75,19 @@ export(crlmm,
75 75
        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
76 76
 export(constructIlluminaCNSet)
77 77
 ##export(linesCNSet)
78
-export(fit.lm1, fit.lm2, fit.lm3, fit.lm4, construct,
79
-       dqrlsWrapper, fit.wls)
80
-export(computeCopynumber, ACN)
81
-export(totalCopyNumber)
78
+##export(fit.lm1, fit.lm2, fit.lm3, fit.lm4, construct,
79
+##       dqrlsWrapper, fit.wls)
80
+export(computeCopynumber, totalCopynumber)
82 81
 export(cnrma, cnrma2)
82
+exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns)
83
+export(genotypeSummary,
84
+       shrinkSummary,
85
+       estimateCnParameters)
86
+##       summarizeSnps,
87
+##       summarizeNps,
88
+##       shrinkGenotypeSummaries,
89
+##       summarizeMaleXGenotypes
83 90
 
84
-exportMethods("A<-", "B<-", "nuA", "nuB", "phiA", "phiB", "nuA<-", "nuB<-", "phiA<-", "phiB<-")
85
-exportMethods(Ns, medians, mads, tau2, corr)
86
-exportClasses(ff_or_matrix)
87
-export(genotypeSummary, summarizeSnps, summarizeNps, shrinkSummary, shrinkGenotypeSummaries, summarizeMaleXGenotypes,
88
-       indexComplete)
89
-export(Ns)
90 91
 ## For debugging
91 92
 ## exportPattern("^[^\\.]")
92 93
 
Browse code

Edits to CA,CB, ACN accessors for copy number

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48961 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/08/2010 02:50:05
Showing1 changed files
... ...
@@ -29,7 +29,7 @@ importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)
29 29
 importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
30 30
 		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,
31 31
 		  chromosome, position, A, B,
32
-		  "A<-", "B<-", open, close, lM, flags,
32
+		  "A<-", "B<-", open, close, flags,
33 33
 		  batchStatistics, "batchStatistics<-", updateObject)
34 34
 
35 35
 
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
Showing1 changed files
... ...
@@ -29,7 +29,9 @@ importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)
29 29
 importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
30 30
 		  "confs<-", cnConfidence, "cnConfidence<-", isSnp,
31 31