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: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@67435 bc3139a8-67e5-0310-9ffc-ced21a209358
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
Merge branch 'collab'

* collab:
  update Rds
  revert imputeGender to original api
  bug fix for calculateRBafCNSet
  update calculateRBafCNSet
  Fix documentation for crlmmCopynumber -- added argument fitLinearModel
  update crlmmGT2
  Put rm(DD, ...) further down in crlmmGT2 function
  remove message about cloning A and B
  Open and close callsPr and callsGt in crlmmGT2 (when args not missing)
  revert removed indices loaded in crlmmGT2
  snprmaAffy no longer writes normalized intensities to calls and callProbability slots. crlmmGT2 takes arguments callsGt and callsPr. When present, crlmmGT2 will not overwrite A and B.
  explicit coercion to matrix in imputeGender
  Assign imputed gender to cnSet$gender within crlmmGT2 function.
  Change sum(SNR > SNRmin) to sum(SNR[] > SNRmin) in imputeGender

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@69450 bc3139a8-67e5-0310-9ffc-ced21a209358