R: Find the location of mutations in a sequence

getMutatedPositions {tigger} | R Documentation

## Find the location of mutations in a sequence

### Description

`getMutatedPositions` takes two vectors of aligned sequences and compares pairs of sequences. It returns a list of the nucleotide positions of any differences.

### Usage

    getMutatedPositions(
      samples,
      germlines,
      ignored_regex = "[\\.N-]",
      match_instead = FALSE
    )

### Arguments

`samples` | vector of strings respresenting aligned sequences
`germlines` | vector of strings respresenting aligned sequences to which `samples` will be compared. If only one string is submitted, it will be used for all `samples`.
`ignored_regex` | regular expression indicating what characters should be ignored (such as gaps and N nucleotides).
`match_instead` | if `TRUE`, the function returns the positions that are the same instead of those that are different.

### Value

A list of the nucleotide positions of any differences between the input vectors.

### Examples

    # Create strings to act as a sample sequences and a reference sequence
    seqs <- c("----GATA", "GAGAGAGA", "TANA")
    ref <- "GATAGATA"

    # Find the differences between the two
    getMutatedPositions(seqs, ref)

[Package tigger version 1.0.0 Index]