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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
Showing 1 changed files

@@ -1,4 +1,5 @@
                                      setOldClass("ellipse")
                                      setOldClass("ffdf")
                                     +##setOldClass("ff_matrix")
                                      ##setClassUnion("ff_or_matrix", c("ffdf", "ff_matrix", "matrix"))
                                      setClass("PredictionRegion", contains="list")

@@ -3,20 +3,3 @@ setOldClass("ff_matrix")
                                      setOldClass("ffdf")
                                      ##setClassUnion("ff_or_matrix", c("ff_matrix", "matrix", "ffdf"))
                                      setClassUnion("ff_or_matrix", c("ff_matrix", "matrix"))
                                     -setClass("CNSetLM", contains="CNSet", representation(lM="list_or_ffdf"))
                                     -setMethod("initialize", "CNSetLM", function(.Object, lM=new("list"), ...){
                                     -	.Object@lM <- lM
                                     -	.Object <- callNextMethod(.Object, ...)
                                     -})
                                     -setValidity("CNSetLM",
                                     -	    function(object){
                                     -		    if(!"batch" %in% varLabels(protocolData(object)))
                                     -			    return("'batch' not defined in protocolData")
                                     -		    if(!"chromosome" %in% fvarLabels(object))
                                     -			    return("'chromosome' not defined in featureData")
                                     -		    if(!"position" %in% fvarLabels(object))
                                     -			    return("'position' not defined in featureData")
                                     -		    if(!"isSnp" %in% fvarLabels(object))
                                     -			    return("'isSnp' not defined in featureData")
                                     -		    return(TRUE)
                                     -	    })

@@ -3,6 +3,4 @@ setOldClass("ff_matrix")
                                      setOldClass("ffdf")
                                      setClassUnion("ff_or_matrix", c("ff_matrix", "matrix", "ffdf"))
                                      setClassUnion("integerOrMissing", c("integer", "missing", "numeric"))
                                     -##setClass("CNSetLM", contains="CNSet", representation(lM="list_or_ffdf"))
                                     -##setClass("CNSetTest", contains="SnpSuperSet")

@@ -2,6 +2,7 @@ setOldClass("ffdf")
                                      setOldClass("ff_matrix")
                                      ##setClassUnion("matrix_or_ff", c("matrix", "ff_matrix"))
                                      setClassUnion("list_or_ffdf", c("list", "ffdf"))
                                     +setClassUnion("ff_or_matrix", c("ff_matrix", "matrix", "ffdf"))
                                      setClass("CNSetLM", contains="CNSet", representation(lM="list_or_ffdf"))
                                      setMethod("initialize", "CNSetLM", function(.Object, CA=new("matrix"), CB=new("matrix"), lM=new("list"), ...){
                                      	.Object <- callNextMethod(.Object, CA=CA, CB=CB, lM=lM, ...)

                                     deleted file mode 100644
@@ -1,74 +0,0 @@
                                     -setOldClass("ffdf")
                                     -setOldClass("ff_matrix")
                                     -setClassUnion("matrix_or_ff", c("matrix", "ff_matrix"))
                                     -setClassUnion("list_or_ffdf", c("list", "ffdf"))
                                     -setClass("CrlmmContainer", contains="eSet",
                                     -	 representation(options="list",
                                     -			genomeAnnotation="ANY",
                                     -			"VIRTUAL"))
+                                    -
                                     -setMethod("show", "CrlmmContainer", function(object){
                                     -	callNextMethod(object)
                                     -	cat("options: \n")
                                     -	print(names(crlmmOptions(object)))
                                     -	cat("\n")
                                     -	cat("genomeAnnotation:", nrow(genomeAnnotation(object)), " rows, ", ncol(genomeAnnotation(object)), " columns\n")
                                     -	print(genomeAnnotation(object)[1:5, ])
                                     -	cat("\n")
                                     -})
                                     -setClass("AlleleSet", contains="CrlmmContainer")
                                     -setClass("CallSet", contains="AlleleSet")
                                     -setClass("CNSet", contains="CallSet",
                                     -	 representation(lM="list_or_ffdf"))
+                                    -
                                     -setClass("IlluminaRGSet", contains="CrlmmContainer")
                                     -setClass("IlluminaXYSet", contains="CrlmmContainer")
+                                    -
                                     -setClass("AffymetrixAlleleSet", contains="AlleleSet")  ##AffymetrixAlleleSet
                                     -setClass("IlluminaAlleleSet", contains="AlleleSet")
                                     -##setClass("AffymetrixBigData", contains="AffymetrixAlleleSet")
                                     -##setClass("AffymetrixSmallData", contains="AffymetrixAlleleSet")
                                     -##setClass("IlluminaSmallData", contains="IlluminaAlleleSet")
                                     -##setClass("IlluminaBigData", contains="IlluminaAlleleSet")
                                     -##setMethod("initialize", "AffymetrixBigData", function(.Object, annotation){
                                     -##	.Object <- callNextMethod(.Object)
                                     -##	if(!missing(annotation)) annotation(.Object) <- annotation
                                     -##	.Object
                                     -##})
                                     -##setClass("AffymetrixCallSet", contains="CallSet")
                                     -##setClass("IlluminaCallSet", contains="CallSet")
                                     -setMethod("initialize", "AlleleSet", function(.Object, alleleA=new("matrix"), alleleB=new("matrix"), ...){
                                     -	.Object <- callNextMethod(.Object, alleleA=alleleA, alleleB=alleleB, ...)
                                     -	storageMode(.Object) <- "environment"
                                     -	.Object
                                     -})
                                     -setMethod("initialize", "CallSet", function(.Object, call=new("matrix"), callProbability=new("matrix"), ...){
                                     -	.Object <- callNextMethod(.Object, call=call, callProbability=callProbability, ...)
                                     -	storageMode(.Object) <- "environment"
                                     -	.Object
                                     -})
                                     -setMethod("initialize", "CNSet", function(.Object, CA=new("matrix"), CB=new("matrix"), lM=new("list"), ...){
                                     -	.Object <- callNextMethod(.Object, CA=CA, CB=CB, lM=lM,...)
                                     -	storageMode(.Object) <- "environment"
                                     -	.Object
                                     -})
                                     -setValidity("AlleleSet", function(object) {
                                     -	assayDataValidMembers(assayData(object), c("alleleA", "alleleB"))
                                     -})
                                     -setValidity("IlluminaRGSet", function(object) {
                                     -	assayDataValidMembers(assayData(object), c("R", "G", "zero"))
                                     -})
                                     -setValidity("IlluminaXYSet", function(object) {
                                     -	assayDataValidMembers(assayData(object), c("X", "Y", "zero"))
                                     -})
+                                    -
                                     -setValidity("CallSet", function(object) {
                                     -	assayDataValidMembers(assayData(object), c("alleleA", "alleleB", "call", "callProbability"))
                                     -})
                                     -setValidity("CNSet", function(object) {
                                     -	assayDataValidMembers(assayData(object), c("alleleA", "alleleB", "call", "callProbability", "CA", "CB"))
                                     -})
+                                    -
+                                    -
+                                    -
+                                    -

                                     deleted file mode 100644
@@ -1,9 +0,0 @@
                                     -##setClass("CNSet", contains="eSet")
                                     -##setClass("CNSet", contains=c("SnpCallSetPlus", "CNSet"))
                                     -setClass("CNSet", contains="SnpCallSetPlus",
                                     -	 representation(emissionPr="array",
                                     -			segmentData="RangedData"))
+                                    -
                                     -##setClass("SegmentSet", contains="CNSet",
                                     -##	 representation(emissionPr="array",
                                     -##			segmentData="data.frame"))

@@ -1,11 +1,7 @@
                                     -## Class definition
                                     -setClass("ABset", contains="eSet",
                                     -	 prototype = prototype(
                                     -	 new("VersionedBiobase",
                                     -	     versions=c(classVersion("eSet"), SnpSet="1.0.0"))))
                                     -setClass("crlmmSet", contains="eSet")
                                     -setClass("CrlmmSetList", contains="list")
                                     -setClass("CopyNumberSet", contains="eSet",
                                     -	 prototype = prototype(
                                     -	 new("VersionedBiobase",
                                     -	     versions=c(classVersion("eSet"), SnpSet="1.0.0"))))
                                     +setClass("CopyNumberSet", contains="SnpLevelSet")
                                     +setClass("CrlmmSet", contains=c("SnpCallSetPlus", "CopyNumberSet"))
                                     +setClass("SnpCallSetPlusFF", contains="SnpCallSetPlus")
                                     +setClass("CrlmmSetFF", contains="CrlmmSet")
                                     +setClass("SegmentSet", contains="CrlmmSet",
                                     +	 representation(emissionPr="array",
                                     +			segmentData="data.frame"))

Merge branch 'collab'

Merge branch 'mymac'

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

Add 'ffdf' to the classes used by 'ff_or_matrix'

importing ff_matrix class from oligoClasses

Removed setValidity method for CNSetLM

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

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

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

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

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

Commented out computation of standard errors for coefficients. Replaced crossprod(solve...) with call to the Fortran library dqrls

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

updated copynumber vignette in inst/scripts. Added example datasets

updates to genotype, crlmmIlluminaRS, and crlmmCopynumber

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

fixed bug in cnrma (dimnames(NP) error)

added genotype function to cnrma-functions. Added AllClasses.R file to set ff_matrix and ffdf classes

roll back to crlmm version 1.5.24

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

updates for compatability with oligoClasses

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

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

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

Fixing problems due to different versions of the source