Man pages for campbio/BAGEL
Novel Mutational Signature Analysis
| add_flank_to_variants | Uses a genome object to find context and add it to the... |
| add_sample_annotations | Adds sample annotation to bagel object with available samples |
| add_variant_type | Generates a variant type table |
| annotate_replication_strand | Add replication strand annotation to SBS variants based on... |
| annotate_transcript_strand | Add transcript strand annotation to SBS variants (defined in... |
| annotate_variant_length | Adds an annotation to the input bagel's variant table with... |
| annotate_variant_type | Annotate variants with variant type ("SBS", "INS", "DEl",... |
| auto_predict_grid | Automatic filtering of signatures for exposure prediction... |
| auto_subset_sigs | Automatic filtering of inactive signatures |
| bagel-class | The primary object for BAGEL that contains all variants,... |
| build_custom_table | Builds a custom table from specified user variants |
| build_standard_table | Builds a standard table from user variants |
| combine_predict_grid | Combine prediction grid list into a result object. Exposure... |
| compare_cosmic_v2 | Compare a result object to COSMIC V2 SBS Signatures... |
| compare_cosmic_v3 | Compare a result object to COSMIC V3 Signatures; Select exome... |
| compare_results | Compare two result files to find similar signatures |
| cosmic_v2_sigs | COSMIC v2 SBS96 Signatures Result Object |
| cosmic_v2_subtype_map | Input a cancer subtype to return a list of related COSMIC... |
| cosmic_v3_dbs_sigs | COSMIC v3 DBS Genome Signatures Result Object |
| cosmic_v3_indel_sigs | COSMIC v3 Indel Genome Signatures Result Object |
| cosmic_v3_sbs_sigs | COSMIC v3 SBS96 Genome Signatures Result Object |
| cosmic_v3_sbs_sigs_exome | COSMIC v3 SBS96 Exome Signatures Result Object |
| count_table-class | Object containing the count table matrices, their names and... |
| create_bagel | Creates a bagel object from a variant table |
| create_dbs_table | Creates and adds a table for standard doublet base... |
| create_sbs192_table | Uses a genome object to find context and generate standard... |
| create_sbs96_table | Uses a genome object to find context and generate standard... |
| create_umap | Create a UMAP data.frame from a result object |
| discover_signatures | Discovers signatures and weights from a table of counts using... |
| drop_annotation | Drops a column from the variant table that the user no longer... |
| extract_count_tables | Extract count tables list from a bagel object |
| extract_variants | Extract variants from mutliple objects |
| extract_variants_from_maf | Extract variants from a maf object |
| extract_variants_from_maf_file | Extracts variants from a maf file |
| extract_variants_from_matrix | Extract variants from matrix or data.frame like objects |
| extract_variants_from_vcf | Extracts variants from a VariantAnnotation VCF object |
| extract_variants_from_vcf_file | Extracts variants from a vcf file |
| generate_result_grid | Generate result_grid from bagel based on annotation and range... |
| get_sample_annotations | Return sample annotation from bagel object |
| get_sample_names | Return samples names for bagel object |
| get_variants | Return variants for bagel object |
| init_sample_annotations | Initialize sample annotation data.table with sample names... |
| jsd | Compare two vectors similarity based on Jensen-Shannon... |
| name_signatures | Return sample from bagel object |
| pipe | Pipe operator |
| plot_exposures | Plots signature weights for each sample |
| plot_exposures_by_annotation | Plots signature weights for each sample gridded by single... |
| plot_full | Complete Plotting of input data |
| plot_sample_counts | Return sample from bagel object |
| plot_sample_reconstruction_error | Plotting Signature Motif counts/spectra |
| plot_signatures | Plotting Signature Motif counts/spectra |
| plot_umap | Plot a UMAP data.frame |
| plot_umap_sigs | Plot a UMAP data.frame |
| predict_exposure | LDA prediction of samples based on existing signatures |
| rc | Reverse complement of a string using biostrings |
| rep_range | Replication Timing Data as GRanges Object |
| Result-class | Object containing deconvolved/predicted signatures, sample... |
| Result_Grid-class | Object containing the result objects generated from the... |
| select_genome | Helper function to load common human or mouse genomes |
| set_sample_annotations | Set sample level annotations for bagel object |
| subset_bagel_by_annotation | Creates a new bagel subsetted to only one value of a sample... |
| subset_bagel_by_counts | Creates a new bagel subsetted to only samples with enough... |
| subset_variant_by_type | Subsets a variant table based on Variant Type |
| subset_variants_by_samples | Return sample from bagel object |
| table_96 | Generates a 96 motif table based on input counts for plotting |
