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

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)

[[1]]
integer(0)

[[2]]
[1] 3 7

[[3]]
[1] 1