importFrom(data.table,data.table)
importFrom(data.table,tables)
importFrom(data.table,setkey)
importFrom(data.table,setkeyv)
importFrom(data.table,key)
importFrom(data.table,as.data.table)
importFrom(data.table,is.data.table)
importFrom(data.table,test.data.table)
importFrom(data.table,":=")
importFrom(data.table,setnames)
importFrom(data.table,rbindlist)
importFrom(seqinr,read.fasta)
importFrom(caret,createFolds)
importFrom(plyr,ddply)
importFrom(plyr,ldply)
importFrom(plyr,.)
importFrom(lattice,levelplot)
importFrom(randomForest,randomForest)
importFrom(ROCR,prediction)
importFrom(ROCR,performance)
importFrom(ROCR,plot)
importFrom(reshape2,acast)
importFrom(protiq,iterateScampi)
importFrom(protiq,runScampi)

export(AbsoluteQuantification,ProteinInference,PeptideInference,APEX,proteotypic,apexFeatures,ALF,cval,import,export,pivot)

S3method(AbsoluteQuantification, default)
S3method(predict, AbsoluteQuantification)
S3method(cval, AbsoluteQuantification)
S3method(print, AbsoluteQuantification)
S3method(plot, AbsoluteQuantification)
S3method(hist, AbsoluteQuantification)
S3method(export, AbsoluteQuantification)

S3method(ProteinInference, default)
S3method(PeptideInference, default)

S3method(APEX, default)
S3method(predict, APEX)
S3method(cval, APEX)
S3method(print, APEX)
S3method(plot, APEX)

S3method(proteotypic, default)

S3method(apexFeatures, default)
S3method(print, apexFeatures)

S3method(ALF, default)

S3method(import, default)

S3method(pivot, default)
S3method(pivot, AbsoluteQuantification)
