Man pages for arendsee/fagin
Annotate Orphan Genes
| config | Get a default configuration object |
| config_alignment-class | Alignment settings and thresholds |
| config_alignment_simulation-class | Simulation parameters |
| config_alignment_thresholds-class | Thresholds for alignment significance |
| config_input-class | Paths to inputs and the focal species name |
| config_orf-class | Settings for Open Reading Frame finding |
| config_synder-class | Settings for Synder |
| derived_input-class | Class containing all data required for a Fagin run |
| derive_genomic_ORFs | Derive mono-exonic ORF intervals from a genome |
| derive_nstring | Derive N-interval table from a genome |
| derive_transcript_ORFs | Derive ORFs from transcripts |
| determine_labels | Merge labels for all species |
| determine_origins | Given a species tree and a set of labels, determine orphan... |
| dgumbel | Gumbel density function |
| dnaregex | Internal function for extracting intervals from pattern... |
| dna_summary-class | Summary of a set of DNA sequences |
| extract_with_complements | Extract DNA intervals, reverse complementing them if they are... |
| faa_summary-class | Summary of a set of protein sequences |
| fagin | fagin: Trace the origins of orphan genes |
| fagin_config-class | The top configuration class |
| fagin_io | Input and output |
| fagin_printer | Special printers |
| fagin_summary | Summarize functions |
| final_protein_residue_counts | Get a table listing the last protein residue proportions for... |
| genomic_composition | Summarize the genomic composition of each species |
| get_species | Get all species in the study |
| get_species_phylogenetic_order | Get the phylogenetic order of species (mostly useful for... |
| get_summaries | Transpose the species data summaries |
| get_synder_count_table | Get summary table of synder search intervals per gene counts |
| get_synder_nsi | Get tables of number of search intervals |
| get_targets | Get the target species from a config object |
| gff_summary-class | Summary of a GFF file |
| granges_summary-class | Summary of a IRanges or GRanges file (without the types of a... |
| initial_protein_residue_counts | Get a table listing the first protein residue counts for each... |
| load_gene_models | Load a GFF file as a GenomicFeatures object |
| make_excel_spreadsheet | Create an excel spreadsheet of fagin results |
| make_fagin_cacher | Build the cacher that will be used inside rmonad |
| make_format_translation_warning | Collate the warnings of a Biostrings::translate function |
| make_genome_table | Tabulate states for each genome |
| make_origin_table | Make a table of the origin summaries for each gene |
| make_query_target_table | Tabulate the query to target relationships |
| make_result_archive | Organize output data into a small archive |
| make_secondary_genewise_table | Make a table of the secondary labels for each query gene |
| make_secondary_labels_table | Summarize secondary labels as a table |
| make_synder_flag_table | Summarize the synder flags for each species |
| make_synder_table | Tabulate states for each genome |
| make_synmap_table | Tabulate states for each genome |
| merge_named_vectors | Merge named vectors into a data.frame |
| number_of_scaffolds | Get a table listing the scaffold count for each species |
| numeric_summary-class | Summary of a numeric vector |
| pgumbel | Gumbel function |
| phase_summary-class | CDS phase summary |
| plot_secondary_labels | Plot the secondary labels |
| primary_data | Load primary data |
| protein_has_internal_stop | Count the internal stop codons in each species protein models |
| qgumbel | Gumbel function |
| run_fagin | Run a Fagin analysis |
| secondary_data | Load secondary data |
| seq_summary-class | Summary of a sequence |
| species_data_files-class | References to each of the RData files for a given species |
| species_meta-class | Data summaries and references to full data for a given... |
| species_summaries-class | Summaries of the data stored for each species |
| synmap_summary-class | Summary of a single synteny map |
| synteny_meta-class | Summaries of every synteny map and references to full data |
| tertiary_data | Load tertiary data |
| validate_config | Validate a configuration |
| yeast_config | Initialize the configuration for the yeast case study |
