Build Mutational-Spectrum Catalogs from Variant Call Format
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Documentation for package ‘mSigSpectra’ version 0.1.3
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| add_seq_context | Add flanking sequence context to a VCF data frame |
| add_transcript_strand | Annotate a VCF data frame with transcript strand information |
| all.abundance | K-mer abundances for density calculations |
| annotate_id_vcf | Annotate an in-memory ID (indel) VCF with sequence context, transcript strand, and COSMIC / Koh indel categories |
| annotate_sbs_or_dbs_vcf | Annotate an SBS or DBS VCF with flanking sequence context and transcript strand |
| annot_vcf_to_476_catalog | Convert an annotated indel VCF to a Koh 476-category catalog |
| annot_vcf_to_83_catalog | Convert an annotated indel VCF to a COSMIC 83-category catalog |
| annot_vcf_to_89_catalog | Convert an annotated indel VCF to a Koh 89-category catalog |
| as_catalog | Turn a numeric matrix into a mutational-spectrum catalog |
| catalog_attrs | Report the attributes of an mSigSpectra catalog |
| catalog_row_order | Return catalog row orders for all supported catalog types |
| categorize_1_justified_indel | Given a indel and its sequence context, categorize it |
| cbind_catalogs | Combine catalogs across samples (column-bind) |
| change_476_type_ids_to_open_intervals | Change 476-type indel category identifiers to use right-open repeat intervals |
| change_89_type_ids_to_open_intervals | Change 89-type indel category identifiers to use right-open repeat intervals |
| check_and_remove_discarded_variants | Check a VCF for common variant-level problems and remove the offenders |
| collapse_catalog | Collapse a higher-resolution catalog to a lower-resolution one |
| infer_trans_ranges | Infer transcript ranges for a reference genome |
| is_catalog | Check whether an object looks like an mSigSpectra catalog |
| justify_id_vcf | Add sequence context and transcript information to an in-memory ID (insertion/deletion) VCF, and confirm that they match the given reference genome |
| justify_indel | Move the notional position of a deletion or insertion as far left as possible. |
| read_catalog | Read a mutational-spectrum catalog from a file |
| read_vcf | Read a VCF file into a data.table, caller-agnostically |
| read_vcfs | Read multiple VCF files |
| segment_simple_cpp | Segment a single indel using Rcpp interface |
| seg_simple | Segment a single indel sequence using Rcpp interface |
| split_vcf | Split a mixed-mutation VCF into SBS / DBS / ID sub-tables |
| subset_catalog | Subset a catalog while preserving attributes |
| trans.ranges | Transcript ranges for transcriptional strand annotation |
| trans.ranges.GRCh37 | Transcript ranges for transcriptional strand annotation |
| trans.ranges.GRCh38 | Transcript ranges for transcriptional strand annotation |
| trans.ranges.GRCm38 | Transcript ranges for transcriptional strand annotation |
| transform_catalog | Transform a catalog between counts and density |
| vcf_to_dbs_catalog | Build a DBS mutational-spectrum catalog from an annotated DBS VCF |
| vcf_to_id_catalog | Build an ID (indel) mutational-spectrum catalog from an annotated ID VCF |
| vcf_to_sbs_catalog | Build an SBS mutational-spectrum catalog from an annotated SBS VCF |
| write_catalog | Write a mutational-spectrum catalog to a file |