Description Usage Arguments Value Examples
compute the reverse-complement of a string of nucleotide bases
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | ## S3 method for class 'factor'
revcomp(
seq,
upper.case = NULL,
complement = TRUE,
reverse = TRUE,
RNA.out = FALSE
)
## S3 method for class 'character'
revcomp(
seq,
upper.case = NULL,
complement = TRUE,
reverse = TRUE,
RNA.out = FALSE
)
## S3 method for class 'list'
revcomp(
seq,
upper.case = NULL,
complement = TRUE,
reverse = TRUE,
RNA.out = FALSE
)
## Default S3 method:
revcomp(
seq,
upper.case = NULL,
complement = TRUE,
reverse = TRUE,
RNA.out = FALSE
)
|
seq |
string. A sequence of nucleotide bases (can handle ambiguous bases) |
upper.case |
logical. Whether to force return of upper (TRUE) or lower (FALSE) case. Default to matching input case. |
complement |
logical. Whether to compute the complementary sequence (defaults to TRUE). |
reverse |
logical. Whether to reverse the order of the sequence (defaults to TRUE). |
RNA.out |
logical. Whether to return sequences as DNA (TRUE) with T or as RNA (FALSE) with U (defaults to FAlSE). |
returns a string, vector, character, or list in the same class as the input sequences
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | # example plot
sequence <- "ATCG"
revcomp(sequence)
sequence <- "atcg"
revcomp(sequence)
sequence <- "AtgaNVVMKSvdbTC"
revcomp(sequence)
sequence <- c("ATACAG", "TATAAT", "TTGACA", "A", "c", "g", "nnn")
revcomp(sequence)
sequence <- list("ATACAG", "TATAAT", "TTGACA", "A", "c", "g", "nnn")
revcomp(sequence)
sequence <- factor("ATACAG", "TATAAT", "TTGACA", "A", "c", "g", "nnn")
revcomp(sequence)
sequence <- "ATCG"
revcomp(sequence, reverse = FALSE)
revcomp(sequence, complement = FALSE)
revcomp(sequence, upper.case = FALSE)
|
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