R/get.allele.R

In kkeenan02/MsatAllele: Visualizes the scoring and binning of microsatellite fragment sizes

get.allele <- function(RefDB, Marker, fragment){
  LocusDBF <- OrderByLocus(RefDB,Marker)
  c1<-(LocusDBF[,2]>=fragment-0.8 & LocusDBF[,2]<=fragment+0.8)
  Checkrange<-LocusDBF[c1,2]
  j<-1
  dif<-0
  Lcheck<-length(Checkrange)
  while(j < Lcheck){
    dif<-Checkrange[j+1]-Checkrange[j]
    if(dif>=0.4)break
    j<-j+1 
  }
  ifelse(j < Lcheck - j, Allrange <- Checkrange[(j+1):Lcheck], 
         Allrange <- Checkrange[1:j])
  Allele.code <- round(median(Allrange), digits = 0)
  ifelse(is.na(Allele.code), round(fragment, digits = 0), Allele.code)
}