revcomp: revcomp

In TomKellyGenetics/tktools: Package of personal utilities

revcomp

Description

compute the reverse-complement of a string of nucleotide bases

Usage

## 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
)

Arguments

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).

Value

returns a string, vector, character, or list in the same class as the input sequences

Examples

# 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)

TomKellyGenetics/tktools documentation built on July 6, 2024, 5:44 a.m.