countDuplicates<-function(interactions,column_names = c("frequencies","frequency"
, "read_counts","count")){
include<-any(column_names %in% names(interactions))
##########################################################
if(include){
column_name<- column_names[column_names %in% names(interactions)][1]
if(is.null(interactions[,column_name]) ){
stop("frequencies column missing")
}
}
##########################################################
else{
column_name <- column_names[1]
interactions[, column_name] <- 1
}
##########################################################
interactions <- interactions[order(interactions$chr1, interactions$locus1_start
, interactions$chr2, interactions$locus2_start), ]
##########################################################
duplicates <- c(duplicated(interactions[, -which(names(interactions) == column_name)]))
cumulative <- c(0, cumsum(interactions[, column_name]))
beforeFirstUnique <- cumulative[!c(duplicates, FALSE)]
result <- interactions[!duplicates, ]
result[, column_name] = diff(beforeFirstUnique)
return(result)
}
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