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
v1.15.14: Export constructAffyCNSet.  Used datadir slot in CNSet object added to v 1.19.39 of oligoClasses
depends on v 1.19.39 of oligoClasses
set default values in summarizeNps
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.
change gender <- unlist(gender) to gender <- unlist(genderList)
contains old process1 call
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
Moved rsprocessCel inside of snprmaAffy for lexical scope. Moved imputeGender inside crlmmGT2 for lexical scope
Fix bug in crlmmGT2 caused by unequal batch sizes
updated cnrmaAffy. Removed cnrma2, cnrma.  cnrmaAffy uses lexical scope
constructAffyCNSet initializes mixtureParams slot of the appropriate dimensions
snprmaAffy no longer initializes mixtureParams object, but accesses this information from the cnSet
Change API for genotypeAffy -- remove mixtureParams argument.  Update call to genotypeAffy in genotype function
update cnrmaAffy.  processCEL2 located inside cnrmaAffy function. Uses lexical scope.
Update CNSet objects in data/ with datadir slot and protocolData(object)$filename
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: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@67826 bc3139a8-67e5-0310-9ffc-ced21a209358