#
#import(methods, Biobase, AnnotationDbi)
#
#importFrom(graphics, plot)
#
#importFrom(BiocGenerics, updateObject)
#
#importMethodsFrom(Biobase, exprs)
#
##importClassesFrom(GSEABase, GeneSet)
#
#Generated by codetoolsBioC version 0.0.16
#Timestamp: Mon Dec 19 12:02:49 2011

#Imports: AnnotationDbi, Biobase, BiocGenerics, genefilter, graphics,
#         Matrix, methods, snpStats, stats, utils

importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet,
                  ExpressionSet, MIAxE, Versions)

importClassesFrom(methods, ANY, call, character, environment, list,
                  missing, numeric, oldClass)

importClassesFrom(snpStats, SnpMatrix)

importMethodsFrom(AnnotationDbi, colnames, get, keys, mget, ncol, nrow,
                  revmap)

importMethodsFrom(Biobase, annotation, "annotation<-", assayData,
                  experimentData, "experimentData<-", exprs,
                  featureData, featureNames, pData, phenoData,
                  "phenoData<-", protocolData, "protocolData<-",
                  sampleNames)


exportClasses(
 # primary integrative container
  "smlSet", # "fsmlSet",
 # primary snp metadata container
#  "snpLocs",
 # screening result holders
  "gwSnpScreenResult", 
#"multiGwSnpScreenResult",
  "cwSnpScreenResult", 
#"filteredGwSnpScreenResult",
#   "filteredMultiGwSnpScreenResult", 
 # casting 
  "chrnum", "rsid", "cnumOrMissing", "genesym", "probeId",
   "phenoVar",
#   "filteredMultiGwSnpScreenResult", 
"snpdepth",
 # sessionInfo
   "SessionInfo", "smlSummary", "multiCisTestResult")

exportMethods( "chrnum", "rsid", "genesym", "[",
    "show", "smList", "smlEnv", "probeId",
#    "snpLocs.Hs", 
    "exprs", "[", "plot_EvG", "snpNames", 
#"getSnpLocs",
    "phenoVar", "plot",
    "plot_EvG2", "combine", "getAlleles", "snps", "coerce", "updateObject")

export("rsid", "snpdepth", "chrnum", "probeId", #"snpsNear",
  "smlSummary", "MAFfilter", "featureFilter", "make_smlSet", #"snpLocs.Hsapiens", 
"GTFfilter", "getSS", "exprs")
