Hi, I have a DNAStringSet list and I would like to convert it in a character vector but as.character does not work because it gives me a vector of "<S4 object of class \"DNAStringSet\">".

Could you help me?

Thank you.

Riccardo

I guess you have something like

a = DNAStringSet(c("AAA", "TTT"))
b = DNAStringSet(c("GGG", "CCC"))
dsl = DNAStringSetList(a, b)

which displays as

> dsl
DNAStringSetList of length 2
[[1]] AAA TTT
[[2]] GGG CCC

You could unlist this and coerce

> as.character(unlist(dsl))
[1] "AAA" "TTT" "GGG" "CCC"

but that removes the grouping of DNA strings. Another option is to coerce to a CharacterList, which behaves like a plain-old-list where each element is a character vector.

> cl = as(dsl, "CharacterList")
> cl
CharacterList of length 2
[[1]] AAA TTT
[[2]] GGG CCC

Or make this into a plain-old-list

> as.list(cl)
[[1]]
[1] "AAA" "TTT"

[[2]]
[1] "GGG" "CCC"

But I guess the question is, why do you want to do this? Maybe the step is unnecessary.

Thank you! I want to do this because I have to do a merge between two data frame, in one of them there is a column with character values and in the other table there is another column with DNAStringSet values.

Riccardo