Make a DNA/RNA sequence unambiguous by stripping out all symbols that do
not uniquely specify nucleic acids. In other words, remove all symbols
other than a's, c's, g's, t's or u's from the
sequence.
# S3 method for default
disambiguate(x, case=c("lower", "upper", "as is"), ...)
# S3 method for SeqFastadna
disambiguate(x, ...)
# S3 method for list
disambiguate(x, ...)According to the input x, a character vector, SeqFastadna object or list
containing the completely unambiguous sequence(s) in x.
A character vector, an object that can be coersed to a character vector or a
list of objects that canbe be converted to character vectors. this argument
can also be a SeqFastadna object provided by the seqinr package.
Determines how symbols in x should be treated before translating them
into their complements. “lower”, the default behaviour, converts
all symbols to lowercase while “upper” converts them to
uppercase. “as is” allows the symbols to pass unchanged so that the case
of each output symbol matches that of the corresponding input symbol.
Arguments to be passed from or to other functions.
Andrew Hart and Servet Martínez
If x is a SeqFastadna object or a character vector in which each element
is a single nucleobase, then it represents a single sequence. It will be made
unambiguous and returned in the same form.
On the other hand, if x is a vector of character strings, each of which
represents a nucleic sequence, then the result will bea a character vector in
which each element contains the unambiguous sequence corresponding to the
element in x as a character string.