Package index • refdb

Import
`refdb_import_NCBI()`	Download and import NCBI Nucleotide records
`refdb_set_fields_NCBI()` `refdb_set_fields_BOLD()` `refdb_set_fields_PR2()` `refdb_set_fields_diatbarcode()`	Functions to set fields for various databases
`refdb_set_fields()`	Associate columns to fields
`refdb_set_ncbitax()`	Replace the current taxonomy using the NCBI Taxonomy database
`refdb_get_fields()`	Get fields of a reference database
`refdb_merge()`	Merge reference databases
Clean
`refdb_clean_seq_crop_primers()`	Crop genetic sequences with a set of primers
`refdb_clean_seq_remove_gaps()`	Remove gaps from genetic sequences
`refdb_clean_seq_remove_sideN()`	Remove repeated side N from genetic sequences
`refdb_clean_tax_NA()`	Convert missing taxonomic names to NA
`refdb_clean_tax_harmonize_nomenclature()`	Harmonize taxonomic name nomenclature
`refdb_clean_tax_remove_blank()`	Remove blank characters from taxonomic names
`refdb_clean_tax_remove_extra()`	Remove extra words from taxonomic names
`refdb_clean_tax_remove_subsp()`	Remove subspecific information from taxonomic names
`refdb_clean_tax_remove_uncertainty()`	Remove terms indicating uncertainty in taxonomic names
Filter
`refdb_filter_ref_scope()`	Filter records by taxonomic scope of studies
`refdb_filter_seq_ambiguous()`	Filter sequences based on their number of ambiguous character.
`refdb_filter_seq_duplicates()`	Filter duplicated sequences.
`refdb_filter_seq_homopolymers()`	Filter sequences based on their number of repeated character.
`refdb_filter_seq_length()`	Filter sequences based on their number of character.
`refdb_filter_seq_primer()`	Filter sequences based on the presence of primers.
`refdb_filter_seq_stopcodon()`	Filter sequences based on their number of of stop codons.
`refdb_filter_tax_na()`	Filter records NA taxa
`refdb_filter_tax_precision()`	Filter records based on their taxonomic precision.
Plot
`refdb_plot_map()`	Plot an interactive map
`refdb_plot_seqlen_hist()`	Plot an histogram of sequence lengths
`refdb_plot_tax_barplot()`	Barplots of the number of records for the most represented taxa
`refdb_plot_tax_tree()`	Reference database taxonomy tree
`refdb_plot_tax_treemap()`	Reference database treemap
Check
`refdb_check_seq_conflict()`	Check for conflicts in sequences
`refdb_check_seq_homogeneity()`	Check for genetic homogeneity of taxa
`refdb_check_tax_conflict()`	Check for conflicts in taxonomy
`refdb_check_tax_typo()`	Check for typos in taxonomic names
Report
`refdb_report()`	Compile a report with different checks
Export
`refdb_export_dada2()`	Export reference database for DADA2
`refdb_export_idtaxa()`	Export reference database for DECIPHER (IDTAXA)
`refdb_export_mothur()`	Export reference database for Mothur
`refdb_export_utax()`	Export reference database for USEARCH/VSEARCH
`refdb_write_fields()`	Write fields to a file
Sample
`refdb_sample_tax()`	Sample records within taxa
Fill
`refdb_fill_tax_downstream()`	Fill missing data in taxonomy
`refdb_fill_tax_upstream()`	Fill missing data in taxonomy
Internals
`check_fields()`	Internal check for fields
`.filter_seq_length()`	Scores for filtering operations
`get_ncbi_taxonomy()`	Get NCBI taxonomy
`igraph_from_taxo()`	Create a graph from a taxonomic table
`make_ncbi_table()`	Parse NCBI XML and make a table
`ncbi_taxo_rank()`	Taxonomic ranks of the NCBI Taxonomy database
`process_geo_ncbi()`	Process coordinate column returned by NCBI
`valid_taxo_rank()`	Ranks considered as valid by refdb
`xml_extract()`	Extract XML elements

Reference

Import

Clean

Filter

Plot

Check

Report

Export

Sample

Fill

Internals