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Reverse sequences if needed (merge_methylation_with_metadata() helper)

Source: R/merge_with_metadata.R
reverse_sequence_if_needed.Rd

This function takes a vector of DNA/RNA sequences and a vector of directions (which must all be either "forward" or "reverse", not case-sensitive) and returns a vector of forward DNA/RNA sequences.

Sequences in the vector that were forward to begin with are unchanged, while sequences that were reverse are reverse-complemented via reverse_complement() to produce the forward sequence.

Called by merge_methylation_with_metadata() to create a forward dataset, alongside reverse_quality_if_needed(), reverse_locations_if_needed() and reverse_probabilities_if_needed().

Usage

reverse_sequence_if_needed(
  sequence_vector,
  direction_vector,
  output_mode = "DNA"
)

Arguments

sequence_vector

character vector. The DNA or RNA sequences to be reversed, e.g. c("ATCG", "GGCGGC", "AUUAUA"). Accepts DNA, RNA, or mixed input.

direction_vector

character vector. Whether each sequence is forward or reverse. Must contain only "forward" and "reverse", but is not case sensitive. Must be the same length as sequence_vector.

output_mode

character. Whether reverse-complemented sequences should be converted to DNA (i.e. A complements to T), RNA (i.e. A complements to U), or not complemented at all. Must be "DNA" (default), "RNA", or "reverse_only" to reverse sequence order without complementing. Only affects reverse-complemented sequences. Sequences that were forward to begin with are not altered.

Value

character vector. A vector of all forward versions of the input sequence vector.

Examples

reverse_sequence_if_needed(
    sequence_vector = c("TAAGGC", "TAAGGC"),
    direction_vector = c("reverse", "forward")
)
#> [1] "GCCTTA" "TAAGGC"

reverse_sequence_if_needed(
    sequence_vector = c("UAAGGC", "UAAGGC"),
    direction_vector = c("reverse", "forward"),
    output_mode = "RNA"
)
#> [1] "GCCUUA" "UAAGGC"

reverse_sequence_if_needed(
    sequence_vector = c("TAAGGC", "TAAGGC"),
    direction_vector = c("reverse", "forward"),
    output_mode = "reverse_only"
)
#> [1] "CGGAAT" "TAAGGC"