OrientNucleotides {DECIPHER} | R Documentation

## Orient Nucleotide Sequences

### Description

Orients nucleotide sequences to match the directionality and complementarity of specified reference sequences.

### Usage

    OrientNucleotides(myXStringSet,
                      reference = which.max(width(myXStringSet)),
                      type = "sequences",
                      orientation = "all",
                      threshold = 0.05,
                      verbose = TRUE,
                      processors = 1)

### Arguments

`myXStringSet` | A `DNAStringSet` or `RNAStringSet` of unaligned sequences.
`reference` | The index of reference sequences with the same (desired) orientation. By default the first sequence with maximum width will be used.
`type` | Character string indicating the type of results desired. This should be (an abbreviation of) either `"sequences"`, `"orientations"`, or `"both"`.
`orientation` | Character string(s) indicating the allowed reorientation(s) of non-reference sequences. This should be (an abbreviation of) either `"all"`, `"reverse"`, `"complement"`, and/or `"both"` (for reverse complement).
`threshold` | Numeric giving the decrease in k-mer distance required to adopt the alternative orientation.
`verbose` | Logical indicating whether to display progress.
`processors` | The number of processors to use, or `NULL` to automatically detect and use all available processors.

### Details

Biological sequences can sometimes have inconsistent orientation that interferes with their analysis. `OrientNucleotides` will reorient sequences by changing their directionality and/or complementarity to match specified `reference` sequences in the same set. The process works by finding the k-mer distance between the reference sequence(s) and each allowed `orientation` of the sequences. Alternative orientations that lessen the distance by at least `threshold` are adopted. Note that this procedure requires a moderately similar `reference` sequence be available for each sequence that needs to be reoriented. Sequences for which a corresponding reference is unavailable will most likely be left alone because alternative orientations will not pass the `threshold`. For this reason, it is recommended to specify several markedly different sequences as `reference`s.

### Value

`OrientNucleotides` can return two types of results: the relative orientations of sequences and/or the reoriented sequences. If `type` is `"sequences"` (the default) then the reoriented sequences are returned. If `type` is `"orientations"` then a character vector is returned that specifies whether sequences were reversed (`"r"`), complemented (`"c"`), reversed complemented (`"rc"`), or in the same orientation (`""`) as the reference sequences (marked by `NA`). If `type` is `"both"` then the output is a list with the first component containing the `"orientations"` and the second component containing the `"sequences"`.

### Author(s)

Erik Wright eswright@pitt.edu

### See Also

`CorrectFrameshifts`

### Examples

    db <- system.file("extdata", "Bacteria_175seqs.sqlite", package="DECIPHER")
    dna <- SearchDB(db, remove="all")
    DNA <- dna # 175 sequences

    # reorient subsamples of the first 169 sequences
    s <- sample(169, 30)
    DNA[s] <- reverseComplement(dna[s])
    s <- sample(169, 30)
    DNA[s] <- reverse(dna[s])
    s <- sample(169, 30)
    DNA[s] <- complement(dna[s])

    DNA <- OrientNucleotides(DNA, reference=170:175)
    DNA==dna # all were correctly reoriented

[Package DECIPHER version 2.16.1 Index]