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 allsamples
. - 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