complement | R Documentation |
Creates the complementary sequence from a given RNA or DNA sequence. The function keeps the type of sequence intact.
complement(x, ...) ## S3 method for class 'sq_dna_bsc' complement(x, ..., NA_letter = getOption("tidysq_NA_letter")) ## S3 method for class 'sq_dna_ext' complement(x, ..., NA_letter = getOption("tidysq_NA_letter")) ## S3 method for class 'sq_rna_bsc' complement(x, ..., NA_letter = getOption("tidysq_NA_letter")) ## S3 method for class 'sq_rna_ext' complement(x, ..., NA_letter = getOption("tidysq_NA_letter"))
x |
[ |
... |
further arguments to be passed from or to other methods. |
NA_letter |
[ |
This function matches elements of sequence to their complementary letters.
For unambiguous letters, "C
" is matched with "G
" and "A
"
is matched with either "T
" (thymine) or "U
" (uracil), depending
on whether input is of dna or rna type.
Ambiguous letters are matched as well, for example "N
" (any
nucleotide) is matched with itself, while "B
" (not alanine) is matched
with "V
" (not thymine/uracil).
sq
object of the same type as input but
built of nucleotides complementary to those in the entered sequences.
sq
Functions interpreting sq in biological context:
%has%()
,
find_motifs()
,
translate()
# Creating DNA and RNA sequences to work on: sq_dna <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT"), alphabet = "dna_bsc") sq_rna <- sq(c("BRAUDUG", "URKKBKUCA", "ANKRUGBNNG", "YYAUNAAAG"), alphabet = "rna_ext") # Here complement() function is used to make PCR (Polymerase Chain Reaction) # primers. Every sequence is rewritten to its complementary equivalent as # in the following example: AAATTTGGG -> TTTAAACCC. complement(sq_dna) complement(sq_rna) # Each sequence have now a complementary equivalent, which can be helpful # during constructing PCR primers.
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