#useDynLib(MEDIPS)
exportPattern("^[[:alpha:]]+")
exportMethods(
    "sample_name",
    "genome_name",
    "number_regions",
    "chr_names",
    "chr_lengths",
    "genome_count",
    "extend",    
    "show",
    "window_size",
    "shifted",
    "uniq"
)
exportClasses(
    "MEDIPSset", 
    "COUPLINGset" 
)
importClassesFrom(methods, character, numeric)
importMethodsFrom(Biostrings, alphabetFrequency, countPDict, matchPattern, PDict, reverseComplement, vcountPattern)
importMethodsFrom(BSgenome, getSeq)
importMethodsFrom(IRanges, cor, end, quantile, ranges, "ranges<-", resize, restrict, space, start, values, var, width,unique,as.vector)
importMethodsFrom(methods, show)
importFrom(Biostrings, DNAString, DNAStringSet)
importFrom(BSgenome, bsapply)
importFrom(graphics, abline, legend, lines, plot)
importFrom(gtools, mixedsort)
importFrom(IRanges, IRanges)
importFrom(stats, lm, t.test, wilcox.test)
importFrom(utils, read.table, setTxtProgressBar, txtProgressBar,write.table)
importFrom(Rsamtools, scanBam,ScanBamParam,scanBamFlag)
importFrom(DNAcopy,CNA,segment,smooth.CNA,getbdry)
importFrom(biomaRt,useMart,getBM)
importFrom(GenomicRanges, countOverlaps, GRanges)
importFrom(preprocessCore, normalize.quantiles)
