.collapse_mirs function is not used anywhere

[bounlu]

I am wondering the purpose of .collapse_mirs function which is not used anywhere.

isomiRs/R/internal.R

Lines 284 to 319 in 8f953e5

	# Collapse isomiRs in miRNAs
	.collapse_mirs <- function(table, ref=FALSE, iso5=FALSE, iso3=FALSE,
	add=FALSE, snv=FALSE, seed=FALSE){
	label <- table$mir
	freq <- id <- NULL
	if (ref == TRUE){
	ref.val <- do.call(paste, table[,4:7])
	ref.val[grep("[ATGC]", ref.val, invert=TRUE,
	ignore.case = TRUE)] <- "ref"
	ref.val[grep("[ATGC]", ref.val, ignore.case = TRUE)] <- "iso"
	label <- paste(label, ref.val, sep=".")
	}
	if (iso5 == TRUE){
	label <- paste(label, table[,"t5"], sep=".t5:")
	}
	if (seed == TRUE){
	seed.val <- as.character(table[,"mism"])
	seed.val[grep("^[2-8][ATGC]", seed.val, invert=TRUE)] <- "0"
	label <- paste(label, seed.val, sep=".seed:")
	}
	if (iso3 == TRUE){
	label <- paste(label, table[,"t3"], sep=".t3:")
	}
	if (add == TRUE){
	label <- paste(label, table[,"add"], sep=".ad:")
	}
	if (snv == TRUE){
	label <- paste(label, table[,"mism"], sep=".mm:")
	}
	table$id <- label
	table.out <- as.data.frame(table %>% group_by(id) %>%
	summarise(total=sum(freq)))
	table.out[is.na(table.out)] <- 0
	table.out
	}