aligned_sequence_matrix_characterizer: Quality check graphics for DNA Barcodes

In carvajalc/BarcoR: Quality Check Graphics for DNA Barcodes

Description

Provide a quality summary of DNA barcodes

Usage

aligned_sequence_matrix_characterizer(
  sequence_fasta_file_user = NULL,
  seqinr_translate_logical_user = TRUE,
  seqinr_genetic_code_user = 1,
  consensus_selection_format_value = c("global", "threshold", "selected_taxa"),
  consensus_selection_threshold_value = 1500,
  consensus_selection_taxa_names_value = NULL,
  consensus_nucleotide_gap_char_value = "-",
  consensus_aminoacid_gap_char_value = "X",
  file_out_user = NULL,
  out_directory_user = NULL
)

Arguments

sequence_fasta_file_user	An aligment o DNA barcodes in fasta file.
seqinr_translate_logical_user	Logical. If it is TRUE the nucleotides will translate into Aminoacids
seqinr_genetic_code_user	Character. A selection of Genetic code ("standard", "vertebrate.mitochondrial", "yeast.mitochondrial", "protozoan.mitochondrial+mycoplasma", "invertebrate.mitochondrial", "ciliate+dasycladaceal", "echinoderm+flatworm.mitochondrial", "euplotid", "bacterial+plantplastid", "alternativeyeast", "ascidian.mitochondrial", "alternativeflatworm.mitochondrial", "blepharism", "chlorophycean.mitochondrial", "trematode.mitochondrial", "scenedesmus.mitochondrial", "thraustochytrium.mitochondria", "Pterobranchia.mitochondrial", "CandidateDivision.SR1+Gracilibacteria", "Pachysolen.tannophilus")
consensus_selection_format_value	Character.compare with consensus based in ("global","threshold", "selected_taxa")
consensus_selection_threshold_value	numeric. A threshold value to conserv in analysis.
consensus_selection_taxa_names_value	Character. A list of taxa names to filter the sequence data.
consensus_nucleotide_gap_char_value	A character indicating the gap value in DNA sequence data , for example "-".
consensus_aminoacid_gap_char_value	A character indicating the gap value in AA data , for example "X".
file_out_user	Character. an optional name to be added to the output file.
out_directory_user	Output directory

Value

4 files: list of ambiguities,codons gaps and quality of DNA barcodes in txt format

Examples

COX1_UVI_quality <- aligned_sequence_matrix_characterizer (sequence_fasta_file_user = system.file("extdata","COI_ordered_nucleotide2.fasta",package="BarcoR"),
                                        seqinr_translate_logical_user = TRUE,
                                        seqinr_genetic_code_user = 2,
                                        consensus_selection_format_value = "selected_taxa",
                                        consensus_selection_threshold_value = 1500,
                                        consensus_selection_taxa_names_value = c("Mannophryne_collaris_COX1_MT627188", "Mannophryne_trinitatis_COX1_JX564878",
                                        "Anomaloglossus_baeobatrachus_COX1_MK069969", "Anomaloglossus_leopardus_COX1_MK069970", "Anomaloglossus_blanci_COX1_MG264895",
                                        "Anomaloglossus_blanci_COX1_NC_037857", "Anomaloglossus_degranvillei_COX1_MG264892", "Anomaloglossus_dewynteri_COX1_MG264891",
                                        "Anomaloglossus_surinamensis_COX1_MG264890", "Rheobates_palmatus_COX1_MT627206", "Allobates_trilineatus_COX1_MT627185",
                                        "Allobates_sumtuosus_COX1_MT627177", "Allobates_amissibilis_COX1_MT627204", "Allobates_marchesianus_COX1_MT627180",
                                        "Allobates_melanolaemus_COX1_MT627203", "Allobates_paleovarzensis_COX1_MT627194", "Allobates_tinae_COX1_MT627190",
                                        "Allobates_granti_COX1_MT627176", "Allobates_chalcopis_COX1_MT627182", "Allobates_conspicuus_COX1_MT627186",
                                        "Allobates_insperatus_COX1_MT627193", "Allobates_gasconi_COX1_MT627191", "Allobates_tapajos_COX1_MT627175",
                                        "Allobates_caeruleodactylus_COX1_MT627199", "Allobates_grillisimilis_COX1_MT627200", "Allobates_crombiei_COX1_MT627174",
                                        "Allobates_goianus_COX1_MT627207", "Allobates_carajas_COX1_MT627183", "Allobates_masniger_COX1_MT627198",
                                        "Allobates_nunciatus_COX1_MT627196", "Allobates_flaviventris_COX1_MT627192", "Allobates_magnussoni_COX1_MT627173",
                                        "Allobates_femoralis_COX1_MT627179", "Allobates_talamancae_COX1_MT627205", "Allobates_undulatus_COX1_MT627181",
                                        "Allobates_olfersioides_COX1_MT627202", "Ameerega_hahneli_COX1_MT627178", "Ameerega_hahneli_COX1_MW042031",
                                        "Ameerega_cainarachi_COX1_SRX6044059", "Ameerega_rubriventris_COX1_SRX6044017", "Ameerega_braccata_COX1_SRX6044048",
                                        "Ameerega_trivittata_COX1_SRX6044007", "Ameerega_parvula_COX1_MW042032", "Ameerega_bilinguis_COX1_MW042030",
                                        "Ameerega_silverstonei_COX1_SRX6044019", "Leucostethus_bilsa_COX1_MW042038", "Leucostethus_fugax_COX1_MW042037",
                                        "Silverstoneia_flotator_COX1_MW042039", "Epipedobates_machalilla_COX1_MW042036", "Epipedobates_anthonyi_COX1_MW042033",
                                        "Epipedobates_boulengeri_COX1_MW042034", "Epipedobates_darwinwallacei_COX1_MW042035", "Hyloxalus_craspedoceps_COX1_SRX6044040",
                                        "Hyloxalus_yasuni_COX1_KT221612", "Hyloxalus_subpunctatus_COX1_KY962392", "Dendrobates_fantasticus_ERX4488168",
                                        "Dendrobates_reticulatus_COX1_SRX6044054", "Dendrobates_defleri_COX1_SRX6044045", "Dendrobates_sirensis_ERX4072904",
                                        "Dendrobates_imitator_ERX3197357", "Dendrobates_mysteriosus_COX1_SRX6044024", "Dendrobates_claudiae_COX1_SRX6044029",
                                        "Andinobates_minutus_COX1_SRX6044028", "Dendrobates_sylvaticus_COX1_SRX5894869", "Dendrobates_pumilio_COX1_SRX7846193",
                                        "Dendrobates_galactonotus_COX1_SRX6044050", "Dendrobates_castaneoticus_COX1_SRX6044052",
                                        "Dendrobates_quinquevittatus_COX1_SRX6044056", "Dendrobates_steyermarki_COX1_SRX6044055", "Dendrobates_auratus_COX1_SRX6761101",
                                        "Dendrobates_leucomelas_COX1_SRX6761106", "Dendrobates_tinctorius_COX1_SRX6761107"),
                                         consensus_nucleotide_gap_char_value = "-",
                                         consensus_aminoacid_gap_char_value = "X",
                                         file_out_user = "COI_UVI",
                                         out_directory_user = NULL)

carvajalc/BarcoR documentation built on Dec. 19, 2021, 1:54 p.m.