import(Biobase)
import(RColorBrewer)
import(limma)
import(glmnet)
import(methods)
importFrom(parallel,makeCluster)
importFrom(parallel,stopCluster)
importFrom(parallel,parRapply)
importFrom(parallel,mclapply)
importFrom(matrixStats,colQuantiles)
importFrom(matrixStats,rowSds)
importFrom(gplots,heatmap.2)
importFrom(foreach,'%dopar%')
importFrom(foreach,foreach)
importFrom(Matrix,bdiag)
importFrom("graphics", "abline", "axis", "lines", "plot", "points",
             "polygon")
importFrom("grDevices", "col2rgb", "rgb")
importFrom("stats", "approx", "approxfun", "binomial", "cmdscale",
             "coefficients", "cor", "cor.test", "density", "dist",
             "dnorm", "fisher.test", "glm.fit", "hclust", "lm.fit",
             "median", "model.matrix", "p.adjust", "plogis", "pnorm",
             "prcomp", "predict", "qlogis", "quantile", "residuals",
             "sd", "var")
importFrom("utils", "packageVersion", "read.delim", "read.table",
             "tail")
exportClasses( "MRexperiment" )

exportMethods(
"[",
"colSums",
"rowSums",
"colMeans",
"rowMeans",
"normFactors",
"normFactors<-",
"libSize",
"libSize<-"
)

export(
aggregateByTaxonomy,
aggTax,
aggregateBySample,
aggSamp,
biom2MRexperiment,
calculateEffectiveSamples,
calcNormFactors,
correlationTest,
correctIndices,
cumNorm,
cumNormMat,
cumNormStat,
cumNormStatFast,
expSummary,
exportMat,
exportStats,
fitDO,
fitMeta,
fitFeatureModel,
fitLogNormal,
fitPA,
fitMultipleTimeSeries,
fitSSTimeSeries,
fitTimeSeries,
fitZig,
filterData,
load_biom,
load_meta,
load_metaQ,
load_phenoData,
loadBiom,
loadMeta,
loadMetaQ,
loadPhenoData,
makeLabels,
mergeMRexperiments,
MRcoefs,
MRcounts,
MRfulltable,
MRtable,
MRexperiment2biom,
plotBubble,
plotCorr,
plotGenus,
plotMRheatmap,
plotOTU,
plotOrd,
plotRare,
plotFeature,
plotTimeSeries,
plotClassTimeSeries,
uniqueFeatures,
returnAppropriateObj,
ssFit,
ssIntervalCandidate,
ssPerm,
ssPermAnalysis,
ts2MRexperiment,
trapz,
zigControl,
newMRexperiment,
posteriorProbs
)