getAbundanceThreshold(standardizedDereplicatedSites, 50) hardcoded 50 could be too many for small data set about genetherapypatientreportmaker HOT 2 CLOSED

function(sites, numGenes){
  orderedAbundances <- sites[order(-sites$estAbundProp)]
  #'unique' functionally removes anything that's duplicated, thus preserving order
  abundCutoff <- orderedAbundances$nearest_refSeq_gene==unique(orderedAbundances$nearest_refSeq_gene)[numGenes]
  abundCutoff <- orderedAbundances[which(abundCutoff)[1]]$estAbundProp
  abundCutoff
}

tail(head(, numGenes),1)
abundCutoff <- orderedAbundances$nearest_refSeq_gene==tail(head(unique(orderedAbundances$nearest_refSeq_gene), numGenes), 1)