Importing and processingFunctions to import, extract, and process variants |
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Extract variants from mutliple objects |
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Extract variants from a maf object |
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Extracts variants from a maf file |
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Extract variants from matrix or data.frame like objects |
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Extracts variants from a VariantAnnotation VCF object |
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Extracts variants from a vcf file |
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musica objectsFunctions to create and subset musica objects |
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Helper function to load common human or mouse genomes |
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Creates a musica object from a variant table |
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Creates a new musica object subsetted to only one value of a sample annotation |
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Creates a new musica subsetted to only samples with enough variants |
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Subsets a variant table based on Variant Type |
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Return sample from musica_variant object |
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Retrieve variants from a musica or musica_result object |
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Creating mutation count tablesFunctions to build and combine mutation count tables |
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Builds count tables using various mutation type schemas |
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Builds a custom table from specified user variants |
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Uses a genome object to find context and add it to the variant table |
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Add replication strand annotation to SBS variants based on bedgraph file |
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Add transcript strand annotation to SBS variants (defined in genes only) |
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Adds an annotation to the input musica's variant table with length of each variant |
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Annotate variants with variant type ("SBS", "INS", "DEl", "DBS") |
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Combines tables into a single table that can be used for discovery/prediction |
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Extract count tables list from a musica object |
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Retrieve the list of count_tables from a musica or musica_result object |
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Sample annotationsFunctions to add and manipulate sample annotations |
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Get or set sample annotations from a musica or musica_result object |
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Retrieve sample names from a musica or musica_result object |
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Drops a column from the variant table that the user no longer needs |
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Discovery and predictionFunctions to identify signatures and exposures from mutation count tables |
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Discover mutational signatures |
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Retrieve exposures from a musica_result object |
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Retrieve signatures from a musica_result object |
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Return sample from musica object |
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Automatic filtering of signatures for exposure prediction gridded across specific annotation |
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Combine prediction grid list into a result object. Exposure values are zero for samples in an annotation where that signature was not predicted |
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Generate result_grid from musica based on annotation and range of k |
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VisualizationFunctions to identify signatures and exposures from mutation count tables |
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Display sample exposures with bar, box, or violin plots |
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Plots the mutational signatures |
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Plot a UMAP from a musica result |
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Visualize clustering results |
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Compare exposures of annotated samples |
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Plot heatmaps using the exposures matrix |
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Plot distribution of sample counts |
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Plot reconstruction error for a sample |
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Prediction of exposures in new samples using pre-existing signatures |
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Downstream analysisFunctions to compare the signatures between two results objects |
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Create a UMAP from a musica result |
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Retrieve umap list from a musica_result object |
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Perform clustering analysis from a musica result object |
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Plots for helping decide number of clusters |
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Signature comparisonsFunctions to compare the signatures between two results objects |
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Compare a result object to COSMIC V2 SBS Signatures (combination whole-exome and whole-genome) |
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Compare a result object to COSMIC V3 Signatures; Select exome or genome for SBS and only genome for DBS or Indel classes |
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Compare two result files to find similar signatures |
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Compare exposures of annotated samples |
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COSMIC signaturesResult objects that contain COSMIC signatures |
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COSMIC v2 SBS96 Signatures Result Object |
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COSMIC v3 DBS Genome Signatures Result Object |
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COSMIC v3 Indel Genome Signatures Result Object |
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COSMIC v3 SBS96 Genome Signatures Result Object |
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COSMIC v3 SBS96 Exome Signatures Result Object |
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Miscellaneous functions |
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Input a cancer subtype to return a list of related COSMIC signatures |
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Retrieve musica from a musica_result object |
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Data objects and classes |
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musica_sbs96 |
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musica_sbs96_tiny |
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dbs_musica |
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indel_musica |
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musica |
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musica_annot |
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res |
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res_annot |
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Replication Timing Data as GRanges Object |
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The primary object that contains variants, count_tables, and samples annotations |
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Object containing the count table matrices, their names and descriptions that we generated by provided and by user functions. These are used to discover and infer signatures and exposures. |
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Object containing deconvolved/predicted signatures, sample weights, and the musica object the result was generated from |
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Object containing the result objects generated from the combination of annotations and a range of k values |
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Retrieve the names of count_tables from a musica or musica_result object |
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Starts the musicatk interactive Shiny app |
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Reverse complement of a string using biostrings |
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Retrieve table name used for plotting from a musica_result object |