sequence_selector_and_aligner: Quality check graphics for DNA Barcodes
In carvajalc/BarcoR: Quality Check Graphics for DNA Barcodes

Description Usage Arguments

View source: R/sequence_selector_and_aligner.R

This function performs an alignment using DECIPHER

sequence_selector_and_aligner(
  input_fasta_files_user,
  input_fasta_reference_file_user = NULL,
  reference_taxa_name_user = NULL,
  seqinr_seqtype_user = c("DNA", "AA"),
  do_pairwiseAlignment_user = TRUE,
  pairwiseAlignment_type_user = "global",
  nucleotideSubstitutionMatrix_match_user = 1,
  nucleotideSubstitutionMatrix_mismatch_user = -3,
  nucleotideSubstitutionMatrix_baseOnly_user = FALSE,
  nucleotideSubstitutionMatrix_type_user = "DNA",
  pairwiseAlignment_gapOpening_user = 5,
  pairwiseAlignment_gapExtension_user = 2,
  order_by_pairwiseAlignment_user = c("nmatch", "dissimilarity_distance"),
  pairwiseAlignment_filter_condition_user = "nmatch",
  filter_condition_value_user = 300,
  filter_condition_operator_user = "more",
  retain_top_n_seq_user = NULL,
  degap_before_multialign_user = TRUE,
  do_multipleAligment_user = TRUE,
  aligner_name_user = c("clustalo", "mafft", "DECIPHER"),
  aligner_bin_location_user = NULL,
  aligner_quiet_user = FALSE,
  clustal_n_threads_user = 1,
  muscle_n_iter_user = 16,
  mafft_accuracy_method_user = NULL,
  mafft_retree_user = 2,
  mafft_maxiterate_user = 1000,
  mafft_gap_opening_penalty_user = 1.53,
  mafft_gap_extension_penalty_user = 0.123,
  decipher_iterations_user = 3,
  decipher_refinements_user = 2,
  decipher_gapOpening_user = c(-18, -16),
  decipher_gapExtension_user = c(-2, -1),
  decipher_useStructures_user = TRUE,
  decipher_structures_user = NULL,
  decipher_levels_user = c(0.9, 0.7, 0.7, 0.4, 10, 5, 5, 2),
  file_out_user = NULL,
  out_directory_user = NULL
)

`input_fasta_files_user`	fasta file with sequences to be align
`input_fasta_reference_file_user`	an optional fasta file with a sequence to be used as reference for a pairwise alignment. All parameter related with pairwise alignment are aligment against a reference sequence(s). do_pairwiseAlignment_user must be TRUE
`reference_taxa_name_user`	a optional sequence name(s) to be selected as reference reference sequence in input_fasta_reference_file_user
`seqinr_seqtype_user`	Charater indicating if sequence data are "DNA or "AA"
`do_pairwiseAlignment_user`	Logical. If it is TRUE performs a pairwise alignment with reference sequence in input_fasta_reference_file_user
`pairwiseAlignment_type_user`	Character indicating the type pairwise alignment (see Biostrings::pairwiseAlignment function), example "global"
`nucleotideSubstitutionMatrix_match_user`	Numeric. indicating the parameter match in pairwise alignment (see Biostrings::nucleotideSubstitutionMatrix).
`nucleotideSubstitutionMatrix_mismatch_user`	Numeric indicating the parameter mismatch in pairwise alignment (see Biostrings::nucleotideSubstitutionMatrix).
`nucleotideSubstitutionMatrix_baseOnly_user`	Numeric indicating the parameter baseOnly in pairwise alignment (See Biostrings::nucleotideSubstitutionMatrix).
`nucleotideSubstitutionMatrix_type_user`	Numeric indicating the parameter type in pairwise alignment (See Biostrings::nucleotideSubstitutionMatrix).
`pairwiseAlignment_gapOpening_user`	Numeric. indicating the parameter gapOpening in pairwise alignment (See Biostrings::pairwiseAlignment)
`pairwiseAlignment_gapExtension_user`	Numeric indicating the parameter gapExtension in pairwise alignment (See Biostrings::pairwiseAlignment)
`order_by_pairwiseAlignment_user`	Character indicating the criterion to order the sequence in the pairwise alignment. Example: "nmatch" or based in "dissimilarity_distance"
`pairwiseAlignment_filter_condition_user`	Character indicating the Criterion to filter the sequence in the pairwise alignment. Example: "nmatch" or based in "dissimilarity_distance"
`filter_condition_value_user`	Numeric indicating the filter value in pairwiseAlignment_filter_condition_user
`filter_condition_operator_user`	Character indicating if the filter is performed to values higher "more" than filter_condition_value_user or "less" than filter_condition_value_user
`retain_top_n_seq_user`	Number of sequence to keep based filter condiction against reference sequence in pairwise alignment
`degap_before_multialign_user`	Logical. True remove all gaps in sequence in pairwise alignment
`do_multipleAligment_user`	Logical. True perform a multiple alignment with differents aligners ("clustalo", "mafft", "DECIPHER")
`aligner_name_user`	Character indicating the aligner to use if do_multipleAligment_user is TRUE ("clustalo", "mafft", "DECIPHER")
`aligner_bin_location_user`	path directory where clustal and mafft bin folder are localetd
`aligner_quiet_user`	Logical indicating whether to display alignment progress
`clustal_n_threads_user`	Numeric indicating number of cores to be used in clustal alignment (if proper parameters are activated)
`muscle_n_iter_user`	Numeric indicating Maximum number of iterations in muscle alignment (if proper parameters are activated)
`mafft_accuracy_method_user`	Character indicating Accuracy-oriented methods in maftt alignment. (if proper parameters are activated)
`mafft_retree_user`	Numeric indicating the alignment strategies in mafft alignment. FFT-NS-1 (1) or FFT-NS-2 (2).
`mafft_maxiterate_user`	Numeric indicating the Iterative refinement method (max. 1000) in maftt alignment.
`mafft_gap_opening_penalty_user`	Numeric indicating Gap opening penalty at group-to-group alignment in maftt alignment.
`mafft_gap_extension_penalty_user`	Numeric indicating gap extension penalty maftt alignment.
`decipher_iterations_user`	Number of iteration to perform in DECIPHER alignment. See iterations parameter in DECIPHER::AlignSeqs
`decipher_refinements_user`	Number of refinement to perform in DECIPHER See refinements parameter in DECIPHER::AlignSeqs
`decipher_gapOpening_user`	Numeric indicating cost for opening a gap in the DECIPHER alignment. See gapOpening parameter in DECIPHER::AlignSeqs
`decipher_gapExtension_user`	Numeric indicating cost for extending an open gap in the DECIPHER alignment. See gapExtension parameter in DECIPHER::AlignSeqs.
`decipher_useStructures_user`	Logical indicating whether to use secondary structure predictions during DECIPHER alignment. See UseStructures parameter in DECIPHER::AlignSeqs.
`decipher_structures_user`	Character indicating list of secondary structure probabilities for decipher_useStructures_user. see DECIPHER::AlignSeqs for more details.
`decipher_levels_user`	Numeric with eight elements specifying the levels at which to trigger events. see DECIPHER::AlignSeqs for more details.
`file_out_user`	Character to be added in the output file
`out_directory_user`	output directory