isoCounts for seed=TRUE is void

[bounlu]

Hi,

In the isoCounts function, when seed=TRUE is specified, it does nothing:

ids_counts_all = isoCounts(ids = isomirs, all = TRUE)
ids_counts_seed = isoCounts(ids = isomirs, seed = TRUE)

identical(counts(ids_counts_all), counts(ids_counts_seed))
[1] TRUE

Here is the code:

isomiRs/R/internal.R

Lines 201 to 236 in 8f953e5

	IsoCountsFromMatrix <- function(rawData, des, ref=FALSE, iso5=FALSE,
	iso3=FALSE, add=FALSE,
	snv=FALSE, seed=FALSE, minc=1){
	is_subs = snv & rawData[["mism"]] != "0"
	is_add = add & rawData[["add"]] != "0"
	is_t5 = iso5 & rawData[["t5"]] != "0"
	is_t3 = iso3 & rawData[["t3"]] != "0"
	is_ref = ref & rawData[["mism"]] == "0" & rawData[["add"]] == "0" & rawData[["t5"]] == "0" & rawData[["t3"]] == "0"
	dt <- rawData %>%
	mutate(uid = mir) %>%
	mutate(uid = ifelse(is_ref,
	paste0(uid, paste0(";ref")),
	uid)) %>%
	mutate(uid = ifelse(is_subs,
	paste0(uid, paste0(";iso_snp:", mism)),
	uid)) %>%
	mutate(uid = ifelse(is_add,
	paste0(uid, paste0(";iso_add:", add)),
	uid)) %>%
	mutate(uid = ifelse(is_t5,
	paste0(uid, paste0(";iso_5p:", t5)),
	uid)) %>%
	mutate(uid = ifelse(is_t3,
	paste0(uid, paste0(";iso_3p:", t3)),
	uid)) %>%
	.[,c("uid", rownames(des))] %>%
	group_by(!!sym("uid")) %>%
	summarise_all(sum) %>%
	as.data.frame() %>%
	remove_rownames() %>%
	column_to_rownames("uid") %>%
	as.matrix()
	if (dim(dt)[1] == 0)
	warning("No miRNA found. Make sure the third column of the file has the count value different than 0.")
	dt
	}