A DNA Reference Library Manager

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Documentation for package ‘refdb’ version 0.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

.filter_seq_length	Scores for filtering operations
check_fields	Internal check for fields
fields_dbs	Functions to set fields for various databases
filter_scores	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
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
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_harmonize_nomenclature	Harmonize taxonomic name nomenclature
refdb_clean_tax_NA	Convert missing taxonomic names to NA
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
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_fill_tax_downstream	Fill missing data in taxonomy
refdb_fill_tax_upstream	Fill missing data in taxonomy
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.
refdb_get_fields	Get fields of a reference database
refdb_import_BOLD	Download and import BOLD records
refdb_import_NCBI	Download and import NCBI Nucleotide records
refdb_merge	Merge reference databases
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
refdb_report	Compile a report with different checks
refdb_sample_tax	Sample records within taxa
refdb_set_fields	Associate columns to fields
refdb_set_fields_BOLD	Functions to set fields for various databases
refdb_set_fields_diatbarcode	Functions to set fields for various databases
refdb_set_fields_NCBI	Functions to set fields for various databases
refdb_set_fields_PR2	Functions to set fields for various databases
refdb_set_ncbitax	Replace the current taxonomy using the NCBI Taxonomy database
refdb_write_fields	Write fields to a file
valid_taxo_rank	Ranks considered as valid by refdb
xml_extract	Extract XML elements