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]