Man pages for lijing28101/fagin2
Annotate Orphan Genes
| AA_aln | alignment function |
| add_gene | Do alignment for new genes from focal species agaginst to... |
| align_by_map | alignment function |
| alignToGenome | alignment function |
| aln_xy | alignment function |
| buildFeatureTable | Build table of binary features |
| buildLabelsTree | Build label tree for homolog decision |
| calculate_match_significance | Calculate significance for alignment between focal species... |
| check_for_incomplete_models | Check incomplete gene models |
| check_for_internal_stops | Check internal stop codon |
| check_protein_transcript_match | Check whether the names of protein and mRNA match |
| compare_target_to_focal | Do alignment for the genes from focal species agaginst to... |
| config | Get a default configuration object |
| config_alignment_alnrate-class | Algnment rate thresholds for alignment significance |
| config_alignment-class | Alignment settings and thresholds |
| config_alignment_pvalue-class | P-value thresholds for alignment significance |
| config_alignment_simulation-class | Simulation parameters |
| 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 |
| convert_FaFile_to_XStringSet | Convert fasta file to XStringSet object |
| convert_GRanges_to_SynderGFF | Conver GRanges to synder GFF |
| 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 |
| dgumbel | Gumbel density function |
| dnaregex | Internal function for extracting intervals from pattern... |
| dna_summary-class | Summary of a set of DNA sequences |
| dot-dnaregex_unstranded | Internal function to process strand |
| dot-label | Label |
| extract_phase_from_GRangesList | Extract phase |
| extract_range | extract GRange |
| extract_with_complements | Extract DNA intervals, reverse complementing them if they are... |
| faa_summary-class | Summary of a set of protein sequences |
| fagin_config-class | The top configuration class |
| fagin_io | Input and output |
| fagin_summary | Summarize functions |
| filter_with_warnings__zero_length_proteins | Filter out protein with zero length |
| filter_with_warning__unnamed_entries | Filter uname entries |
| find_indels | Find interval for indel |
| fit.gumbel | Given simulated data, generate functions for assigning... |
| fix_names | fix name from orfik |
| fuzzy_translate | Translate DNA to protein |
| gene_check | Check gene list |
| get_alignment_table | Get alignment info |
| get_dna2dna | alignment function |
| get_gff_from_txdb | Get gff from transcriptome DB |
| get_hits_info | Summary for the gene with significant hits |
| get_logmn | alignment function |
| getORFs | Get ORF |
| get_query_position | Get query gene position |
| get_species | Get all species in the study |
| get_target_mRNA_position | Get target mRNA position |
| get_target_position | Get target gene/ORF position |
| get_trans_dna | Get transcripts sequence from GenomicRanges object |
| gff_summary-class | Summary of a GFF file |
| granges_summary-class | Summary of a IRanges or GRanges file (without the types of a... |
| labelTreeToTable | Match label to feature table |
| load_gene_models | Load gene model |
| load_species | Load sequence and gff for species |
| MakeGI | Make GenomicRanges object |
| make_seqinfo | Make SequenceInfo |
| merge_feature_table | Summarize homolog class for the list of genes from focal... |
| numeric_summary-class | Summary of a numeric vector |
| overlapMap | Find all features in the gff GenomicRanges object that... |
| pgumbel | Gumbel function |
| phase_summary-class | CDS phase summary |
| qgumbel | Gumbel function |
| run_fagin | Run fagin analysis |
| run_fagin_add | Add new gene list to fagin analysis |
| run_fagin_parallel | Run fagin analysis |
| secondary_data | Compare the genes from focal species to target genome and... |
| secondary_data_add | Compare the new genes from focal species to target genome and... |
| 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 |
| trim_CDS_with_non_zero_phase | Trim CDS |
| validate_config | Validate a configuration |
