getMutatedPositions - 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
a vector of strings respresenting aligned sequences
germlines
a 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
a 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)
[[1]]
integer(0)

[[2]]
[1] 3 7

[[3]]
[1] 1