Geographically-Conscious Taxonomic Assignment for Metabarcoding

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Documentation for package ‘LocaTT’ version 1.2.0

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adjust_taxonomies Adjust Taxonomies
binomial_test Binomial Test
blast_command_found Check BLAST Installation
blast_version Get BLAST Version
circle Draw Circle Polygon
contains_wildcards Check Whether DNA Sequences Contain Wildcard Characters
coordinates Generate Circular Coordinates
decode_quality_scores Decode DNA Sequence Quality Scores
detection Grouped Detection Plot
expand_taxonomies Expand Taxonomies
filter_sequences Filter DNA Sequences by PCR Replicates
format_reference_database Format Reference Databases
get_consensus_taxonomy Get Consensus Taxonomy from Taxonomic Strings
get_taxonomic_level Get Specified Taxonomic Level from Taxonomic Strings
get_taxonomies.IUCN Get Taxonomies from IUCN Red List Files
get_taxonomies.species_binomials Get NCBI Taxonomies from Species Binomials
isolate_amplicon Trim DNA Sequences to an Amplicon Region Using Forward and Reverse Primer Sequences
local_taxa_tool Perform Geographically-Conscious Taxonomic Assignment
merge_pairs Merge Forward and Reverse DNA Sequence Reads
proportion Grouped Proportion Plot
read.fasta Read FASTA Files
read.fastq Read FASTQ Files
reverse_complement Get the Reverse Complement of a DNA Sequence
sector Draw Sector Polygon
singular.detection Singular Detection Plot
singular.proportion Singular Proportion Plot
substitute_wildcards Substitute Wildcard Characters in a DNA Sequence
summarize_quality_scores Summarize Quality Scores
template Initiate Template Plot
trim_sequences Trim Target Nucleotide Sequence from DNA Sequences
truncate_and_merge_pairs Truncate and Merge Forward and Reverse DNA Sequence Reads
truncate_sequences.length Truncate DNA Sequences to Specified Length
truncate_sequences.probability Truncate DNA Sequences at Specified Probability that All Bases were Called Correctly
truncate_sequences.quality_score Truncate DNA Sequences at Specified Quality Score
write.fasta Write FASTA Files
write.fastq Write FASTQ Files