What tales_align aligned on and how, kept with the
alignment so that it can be reproduced or interpreted later, for example
to tell whether a tales_msa holding both rvd and
dom_code columns was aligned on its RVDs or on its domain codes.
Subsetting keeps these settings; returning to a plain tales
(as_tales) drops them.
Value
A list with residue_col, the column aligned on;
domain_distances, the scoring given to tales_align()
(NULL, "rvd", or the matrix, table or file supplied);
and mafft_opts, the options MAFFT ran with. NULL for a
tales_msa built by hand with tales_msa.
See also
Other TALE alignment:
as.matrix.tales_msa(),
is_tales_msa(),
tales_align(),
tales_consensus(),
tales_consensus_match(),
tales_msa(),
tales_msa_width(),
validate_tales_msa()
Examples
# \donttest{
# Needs MAFFT, resolved from the tantale conda environment on first use.
rvd_fasta <- system.file("extdata", "TalA_RVDSeqs_AnnoTALE.fasta",
package = "tantale")
msa <- tales_align(as_tales(rvd_fasta, sep = "-"), residue_col = "rvd")
#> Now running MAFFT (Copyright 2002-2007 Kazutaka Katoh) on TALE array sequences.
tales_msa_params(msa)$residue_col
#> [1] "rvd"
# }