bad_arg                 Emit an error message for an invalid function
                        argument (generic 'ggDNAvis' helper)
convert_MM_vector_to_locations
                        Convert MM tag to absolute index locations
                        (deprecated helper)
convert_base_to_number
                        Map a single base to the corresponding number
                        (generic 'ggDNAvis' helper)
convert_locations_to_MM_vector
                        Convert absolute index locations to MM tag
                        ('write_modified_fastq()' helper)
convert_modification_to_number_vector
                        Convert string-ified modification probabilities
                        and locations to a single vector of
                        probabilities ('visualise_methylation()'
                        helper)
convert_sequence_to_numbers
                        Map a sequence to a vector of numbers (generic
                        'ggDNAvis' helper)
convert_sequences_to_matrix
                        Convert vector of sequences to character matrix
                        (generic 'ggDNAvis' helper)
create_image_data       Rasterise a vector of sequences into a
                        numerical dataframe for ggplotting (generic
                        'ggDNAvis' helper)
debug_join_vector_num   Print a numeric vector to console ('ggDNAvis'
                        debug helper)
debug_join_vector_str   Print a character/string vector to console
                        ('ggDNAvis' debug helper)
example_many_sequences
                        Example multiple sequences data
extract_and_sort_methylation
                        Extract methylation information from dataframe
                        for visualisation
extract_and_sort_sequences
                        Extract, sort, and add spacers between
                        sequences in a dataframe
fastq_quality_scores    Vector of the quality scores used by the FASTQ
                        format
format_time_diff        Format a difference between times (generic
                        'ggDNAvis' helper)
ggDNAvis_aliases        'ggDNAvis' aliases
ggDNAvis_shinyapp       Run the interactive 'ggDNAvis' shinyapp
insert_at_indices       Insert blank items at specified indices in a
                        vector ('visualise_many_sequences()' helper)
merge_fastq_with_metadata
                        Merge FASTQ data with metadata
merge_methylation_with_metadata
                        Merge methylation with metadata
monitor                 Continue performance monitoring (generic
                        'ggDNAvis' helper)
monitor_start           Start performance monitoring (generic
                        'ggDNAvis' helper)
rasterise_index_annotations
                        Process index annotations and rasterise to a
                        x/y/layer dataframe (generic 'ggDNAvis' helper)
rasterise_matrix        Rasterise a matrix to an x/y/layer dataframe
                        (generic 'ggDNAvis' helper)
rasterise_probabilities
                        Create dataframe of locations and rendered
                        probabilities ('visualise_methylation()'
                        helper)
read_fastq              Read sequence and quality information from
                        FASTQ
read_modified_fastq     Read modification information from modified
                        FASTQ
resolve_alias           Resolve argument value when aliases are used
                        (generic 'ggDNAvis' helper)
resolve_alias_map       Process an alias map list (generic 'ggDNAvis'
                        helper)
reverse_complement      Reverse complement a DNA/RNA sequence (generic
                        'ggDNAvis' helper)
reverse_locations_if_needed
                        Reverse modification locations if needed
                        ('merge_methylation_with_metadata()' helper)
reverse_probabilities_if_needed
                        Reverse modification probabilities if needed
                        ('merge_methylation_with_metadata()' helper)
reverse_quality_if_needed
                        Reverse qualities if needed
                        ('merge_methylation_with_metadata()' helper)
reverse_sequence_if_needed
                        Reverse sequences if needed
                        ('merge_methylation_with_metadata()' helper)
sequence_colour_palettes
                        Colour palettes for sequence visualisations
string_to_vector        Split a '","'-joined string back to a vector
                        (generic 'ggDNAvis' helper)
strip_leading_at        Strip leading '@' from character vector
vector_to_string        Join a vector into a comma-separated string
                        (generic 'ggDNAvis' helper)
visualise_many_sequences
                        Visualise many DNA/RNA sequences
visualise_methylation   Visualise methylation probabilities for many
                        DNA sequences
visualise_methylation_colour_scale
                        Visualise methylation colour scalebar
visualise_single_sequence
                        Visualise a single DNA/RNA sequence
write_fastq             Write sequence and quality information to FASTQ
write_modified_fastq    Write modification information stored in
                        dataframe back to modified FASTQ
