#Import packages dependencies
import(GenomicFeatures)
import(ggplot2)
import(BiocParallel)
import(methods)
import(Matrix)
import(ggfortify)
import(Biobase)
importFrom(doParallel,registerDoParallel)
importFrom(lme4,glmer)
importFrom(foreach,foreach,"%dopar%")
importFrom(AnnotationDbi,select)
importFrom(GenomicFeatures,exonsBy,intronsByTranscript,isActiveSeq,"isActiveSeq<-")
importFrom(GenomicRanges,GRanges,elementMetadata)
importFrom(IRanges,IRanges,findOverlaps,start,end)
importFrom(BiocGenerics,strand,unlist)
importFrom(Seqinfo,seqinfo,seqlevels,seqnames)
importFrom(utils,write.table,methods)
importFrom(methods,slot,new,setClass,representation,setMethod,slotNames)

importFrom(grDevices,png,dev.off)
importFrom(stats,chisq.test,median,lm,pf,na.exclude,binomial,anova,pchisq,kmeans,p.adjust)
importMethodsFrom(Matrix,as.matrix)
#importMethodsFrom(utils,methods,slot,new,setClass,representation,setMethod,slotNames)
importMethodsFrom(BiocGenerics)
importMethodsFrom(S4Vectors,Rle)


#Export all names
export(
  chrseparate,
  findAlternative,
  findOversnp,
  saveBplot,
  sQTLsFinder,
  Splicingfinder,
  CalSigSNP,
  RatioFromFPKM,
  calSignificant,  # defunct
  MsqtlFinder,  # defunct
  sqtlfinder  # defunct
)

