'Degenerates' amino acid or nucleic sequence by aggregating elements to bigger groups.
degenerate(seq, element_groups)
seq |
|
---|---|
element_groups | encoding of elements: list of groups to which elements of sequence should be aggregated. Must have unique names. |
A character
vector or matrix (if input is a matrix)
containing aggregated elements.
Characters not present in the element_groups
will be converted to NA with a
warning.
l2n
to easily convert information stored in biological sequences from
letters to numbers.
calc_ed
to calculate distance between encodings.
#> sample_seq #> 1 2 3 4 #> 3 1 3 2# aggregate sequence to purins and pyrimidines deg_seq <- degenerate(sample_seq, list(w = c(1, 4), s = c(2, 3))) table(deg_seq)#> deg_seq #> s w #> 4 5